diff --git a/e2e-tests/problems.spec.ts b/e2e-tests/problems.spec.ts
index 59793cf..06aa486 100644
--- a/e2e-tests/problems.spec.ts
+++ b/e2e-tests/problems.spec.ts
@@ -1,11 +1,11 @@
-import { test, testSkipIfWindows } from "./helpers/test_helper";
+import { test } from "./helpers/test_helper";
 import { expect } from "@playwright/test";
 import fs from "fs";
 import path from "path";
 
 const MINIMAL_APP = "minimal-with-ai-rules";
 
-testSkipIfWindows("problems auto-fix - enabled", async ({ po }) => {
+test("problems auto-fix - enabled", async ({ po }) => {
   await po.setUp();
   await po.importApp(MINIMAL_APP);
   await po.expectPreviewIframeIsVisible();
@@ -18,41 +18,35 @@ testSkipIfWindows("problems auto-fix - enabled", async ({ po }) => {
   await po.snapshotMessages({ replaceDumpPath: true });
 });
 
-testSkipIfWindows(
-  "problems auto-fix - gives up after 2 attempts",
-  async ({ po }) => {
-    await po.setUp();
-    await po.importApp(MINIMAL_APP);
-    await po.expectPreviewIframeIsVisible();
+test("problems auto-fix - gives up after 2 attempts", async ({ po }) => {
+  await po.setUp();
+  await po.importApp(MINIMAL_APP);
+  await po.expectPreviewIframeIsVisible();
 
-    await po.sendPrompt("tc=create-unfixable-ts-errors");
+  await po.sendPrompt("tc=create-unfixable-ts-errors");
 
-    await po.snapshotServerDump("all-messages", { dumpIndex: -2 });
-    await po.snapshotServerDump("all-messages", { dumpIndex: -1 });
+  await po.snapshotServerDump("all-messages", { dumpIndex: -2 });
+  await po.snapshotServerDump("all-messages", { dumpIndex: -1 });
 
-    await po.page.getByTestId("problem-summary").last().click();
-    await expect(
-      po.page.getByTestId("problem-summary").last(),
-    ).toMatchAriaSnapshot();
-    await po.snapshotMessages({ replaceDumpPath: true });
-  },
-);
+  await po.page.getByTestId("problem-summary").last().click();
+  await expect(
+    po.page.getByTestId("problem-summary").last(),
+  ).toMatchAriaSnapshot();
+  await po.snapshotMessages({ replaceDumpPath: true });
+});
 
-testSkipIfWindows(
-  "problems auto-fix - complex delete-rename-write",
-  async ({ po }) => {
-    await po.setUp();
-    await po.importApp(MINIMAL_APP);
-    await po.expectPreviewIframeIsVisible();
+test("problems auto-fix - complex delete-rename-write", async ({ po }) => {
+  await po.setUp();
+  await po.importApp(MINIMAL_APP);
+  await po.expectPreviewIframeIsVisible();
 
-    await po.sendPrompt("tc=create-ts-errors-complex");
+  await po.sendPrompt("tc=create-ts-errors-complex");
 
-    await po.snapshotServerDump("all-messages", { dumpIndex: -2 });
-    await po.snapshotServerDump("all-messages", { dumpIndex: -1 });
+  await po.snapshotServerDump("all-messages", { dumpIndex: -2 });
+  await po.snapshotServerDump("all-messages", { dumpIndex: -1 });
 
-    await po.snapshotMessages({ replaceDumpPath: true });
-  },
-);
+  await po.snapshotMessages({ replaceDumpPath: true });
+});
 
 test("problems auto-fix - disabled", async ({ po }) => {
   await po.setUp({ disableAutoFixProblems: true });
diff --git a/src/utils/VirtualFilesystem.ts b/src/utils/VirtualFilesystem.ts
index 4fbc0eb..f876a0f 100644
--- a/src/utils/VirtualFilesystem.ts
+++ b/src/utils/VirtualFilesystem.ts
@@ -5,6 +5,7 @@ import {
   getDyadRenameTags,
   getDyadDeleteTags,
 } from "../ipc/processors/response_processor";
+import { normalizePath } from "../ipc/processors/normalizePath";
 
 import log from "electron-log";
 
@@ -39,7 +40,39 @@ export abstract class BaseVirtualFileSystem {
   protected baseDir: string;
 
   constructor(baseDir: string) {
-    this.baseDir = baseDir;
+    this.baseDir = path.resolve(baseDir);
+  }
+
+  /**
+   * Normalize path for consistent cross-platform behavior
+   */
+  private normalizePathForKey(filePath: string): string {
+    const absolutePath = path.isAbsolute(filePath)
+      ? filePath
+      : path.resolve(this.baseDir, filePath);
+
+    // Normalize separators and handle case-insensitive Windows paths
+    const normalized = normalizePath(path.normalize(absolutePath));
+
+    // Intentionally do NOT lowercase for Windows which is case-insensitive
+    // because this avoids issues with path comparison.
+    //
+    // This is a trade-off and introduces a small edge case where
+    // e.g. foo.txt and Foo.txt are treated as different files by the VFS
+    // even though Windows treats them as the same file.
+    //
+    // This should be a pretty rare occurence and it's not worth the extra
+    // complexity to handle it.
+    return normalized;
+  }
+
+  /**
+   * Convert normalized path back to platform-appropriate format
+   */
+  private denormalizePath(normalizedPath: string): string {
+    return process.platform === "win32"
+      ? normalizedPath.replace(/\//g, "\\")
+      : normalizedPath;
   }
 
   /**
@@ -69,43 +102,49 @@ export abstract class BaseVirtualFileSystem {
   /**
    * Write a file to the virtual filesystem
    */
-  public writeFile(relativePath: string, content: string): void {
+  protected writeFile(relativePath: string, content: string): void {
     const absolutePath = path.resolve(this.baseDir, relativePath);
-    this.virtualFiles.set(absolutePath, content);
+    const normalizedKey = this.normalizePathForKey(absolutePath);
+
+    this.virtualFiles.set(normalizedKey, content);
     // Remove from deleted files if it was previously deleted
-    this.deletedFiles.delete(absolutePath);
+    this.deletedFiles.delete(normalizedKey);
   }
 
   /**
    * Delete a file from the virtual filesystem
    */
-  public deleteFile(relativePath: string): void {
+  protected deleteFile(relativePath: string): void {
     const absolutePath = path.resolve(this.baseDir, relativePath);
-    this.deletedFiles.add(absolutePath);
+    const normalizedKey = this.normalizePathForKey(absolutePath);
+
+    this.deletedFiles.add(normalizedKey);
     // Remove from virtual files if it exists there
-    this.virtualFiles.delete(absolutePath);
+    this.virtualFiles.delete(normalizedKey);
   }
 
   /**
    * Rename a file in the virtual filesystem
    */
-  public renameFile(fromPath: string, toPath: string): void {
+  protected renameFile(fromPath: string, toPath: string): void {
     const fromAbsolute = path.resolve(this.baseDir, fromPath);
     const toAbsolute = path.resolve(this.baseDir, toPath);
+    const fromNormalized = this.normalizePathForKey(fromAbsolute);
+    const toNormalized = this.normalizePathForKey(toAbsolute);
 
     // Mark old file as deleted
-    this.deletedFiles.add(fromAbsolute);
+    this.deletedFiles.add(fromNormalized);
 
     // If the source file exists in virtual files, move its content
-    if (this.virtualFiles.has(fromAbsolute)) {
-      const content = this.virtualFiles.get(fromAbsolute)!;
-      this.virtualFiles.delete(fromAbsolute);
-      this.virtualFiles.set(toAbsolute, content);
+    if (this.virtualFiles.has(fromNormalized)) {
+      const content = this.virtualFiles.get(fromNormalized)!;
+      this.virtualFiles.delete(fromNormalized);
+      this.virtualFiles.set(toNormalized, content);
     } else {
       // Try to read from actual filesystem
       try {
         const content = fs.readFileSync(fromAbsolute, "utf8");
-        this.virtualFiles.set(toAbsolute, content);
+        this.virtualFiles.set(toNormalized, content);
       } catch (error) {
         // If we can't read the source file, we'll let the consumer handle it
         logger.warn(
@@ -116,7 +155,7 @@ export abstract class BaseVirtualFileSystem {
     }
 
     // Remove destination from deleted files if it was previously deleted
-    this.deletedFiles.delete(toAbsolute);
+    this.deletedFiles.delete(toNormalized);
   }
 
   /**
@@ -124,10 +163,15 @@ export abstract class BaseVirtualFileSystem {
    */
   public getVirtualFiles(): VirtualFile[] {
     return Array.from(this.virtualFiles.entries()).map(
-      ([absolutePath, content]) => ({
-        path: path.relative(this.baseDir, absolutePath),
-        content,
-      }),
+      ([normalizedKey, content]) => {
+        // Convert normalized key back to relative path
+        const denormalizedPath = this.denormalizePath(normalizedKey);
+
+        return {
+          path: path.relative(this.baseDir, denormalizedPath),
+          content,
+        };
+      },
     );
   }
 
@@ -135,84 +179,35 @@ export abstract class BaseVirtualFileSystem {
    * Get all deleted file paths (relative to base directory)
    */
   public getDeletedFiles(): string[] {
-    return Array.from(this.deletedFiles).map((absolutePath) =>
-      path.relative(this.baseDir, absolutePath),
-    );
-  }
-
-  /**
-   * Get all files that should be considered (existing + virtual - deleted)
-   */
-  public getAllFiles(): string[] {
-    const allFiles = new Set<string>();
-
-    // Add virtual files
-    for (const [absolutePath] of this.virtualFiles.entries()) {
-      allFiles.add(path.relative(this.baseDir, absolutePath));
-    }
-
-    // Add existing files (this is a simplified version - in practice you might want to scan the directory)
-    // This method is mainly for getting the current state, consumers can combine with directory scanning
-
-    return Array.from(allFiles);
-  }
-
-  /**
-   * Check if a file has been modified in the virtual filesystem
-   */
-  public isFileModified(filePath: string): boolean {
-    const absolutePath = path.isAbsolute(filePath)
-      ? filePath
-      : path.resolve(this.baseDir, filePath);
-
-    return (
-      this.virtualFiles.has(absolutePath) || this.deletedFiles.has(absolutePath)
-    );
-  }
-
-  /**
-   * Clear all virtual changes
-   */
-  public clear(): void {
-    this.virtualFiles.clear();
-    this.deletedFiles.clear();
-  }
-
-  /**
-   * Get the base directory
-   */
-  public getBaseDir(): string {
-    return this.baseDir;
+    return Array.from(this.deletedFiles).map((normalizedKey) => {
+      // Convert normalized key back to relative path
+      const denormalizedPath = this.denormalizePath(normalizedKey);
+      return path.relative(this.baseDir, denormalizedPath);
+    });
   }
 
   /**
    * Check if a file is deleted in the virtual filesystem
    */
   protected isDeleted(filePath: string): boolean {
-    const absolutePath = path.isAbsolute(filePath)
-      ? filePath
-      : path.resolve(this.baseDir, filePath);
-    return this.deletedFiles.has(absolutePath);
+    const normalizedKey = this.normalizePathForKey(filePath);
+    return this.deletedFiles.has(normalizedKey);
   }
 
   /**
    * Check if a file exists in virtual files
    */
   protected hasVirtualFile(filePath: string): boolean {
-    const absolutePath = path.isAbsolute(filePath)
-      ? filePath
-      : path.resolve(this.baseDir, filePath);
-    return this.virtualFiles.has(absolutePath);
+    const normalizedKey = this.normalizePathForKey(filePath);
+    return this.virtualFiles.has(normalizedKey);
   }
 
   /**
    * Get virtual file content
    */
   protected getVirtualFileContent(filePath: string): string | undefined {
-    const absolutePath = path.isAbsolute(filePath)
-      ? filePath
-      : path.resolve(this.baseDir, filePath);
-    return this.virtualFiles.get(absolutePath);
+    const normalizedKey = this.normalizePathForKey(filePath);
+    return this.virtualFiles.get(normalizedKey);
   }
 }