diff --git a/packages/angular-cli/models/webpack-build-typescript.ts b/packages/angular-cli/models/webpack-build-typescript.ts
index d23ad7ab074c..b574f56bc9bc 100644
--- a/packages/angular-cli/models/webpack-build-typescript.ts
+++ b/packages/angular-cli/models/webpack-build-typescript.ts
@@ -61,9 +61,9 @@ export const getWebpackAotConfigPartial = function(projectRoot: string, appConfi
     plugins: [
       new NgcWebpackPlugin({
         project: path.resolve(projectRoot, appConfig.root, appConfig.tsconfig),
-        baseDir: path.resolve(projectRoot, ''),
+        baseDir: path.resolve(projectRoot, appConfig.root),
         main: path.join(projectRoot, appConfig.root, appConfig.main),
-        genDir: path.resolve(projectRoot, '')
+        genDir: path.resolve(projectRoot, appConfig.root)
       }),
     ]
   };
diff --git a/packages/webpack/src/compiler_host.ts b/packages/webpack/src/compiler_host.ts
index a65c46053896..a97e0c57d265 100644
--- a/packages/webpack/src/compiler_host.ts
+++ b/packages/webpack/src/compiler_host.ts
@@ -91,6 +91,7 @@ export class WebpackCompilerHost implements ts.CompilerHost {
   private _delegate: ts.CompilerHost;
   private _files: {[path: string]: VirtualFileStats} = Object.create(null);
   private _directories: {[path: string]: VirtualDirStats} = Object.create(null);
+  private _changed = false;
 
   constructor(private _options: ts.CompilerOptions, private _setParentNodes = true) {
     this._delegate = ts.createCompilerHost(this._options, this._setParentNodes);
@@ -104,10 +105,15 @@ export class WebpackCompilerHost implements ts.CompilerHost {
       this._directories[p] = new VirtualDirStats(p);
       p = dirname(p);
     }
+
+    this._changed = true;
   }
 
   populateWebpackResolver(resolver: any) {
     const fs = resolver.fileSystem;
+    if (!this._changed) {
+      return;
+    }
 
     for (const fileName of Object.keys(this._files)) {
       const stats = this._files[fileName];
@@ -121,6 +127,8 @@ export class WebpackCompilerHost implements ts.CompilerHost {
       fs._statStorage.data[path] = [null, stats];
       fs._readdirStorage.data[path] = [null, files.concat(dirs)];
     }
+
+    this._changed = false;
   }
 
   fileExists(fileName: string): boolean {
diff --git a/packages/webpack/src/plugin.ts b/packages/webpack/src/plugin.ts
index 92201ad1c9d8..1877d11b06d4 100644
--- a/packages/webpack/src/plugin.ts
+++ b/packages/webpack/src/plugin.ts
@@ -98,14 +98,15 @@ export class NgcWebpackPlugin {
           return callback();
         }
 
-        result.resource = this.genDir;
-        result.recursive = true;
-        result.dependencies.forEach((d: any) => d.critical = false);
-        result.resolveDependencies = createResolveDependenciesFromContextMap((_: any, cb: any) => {
-          return cb(null, this.lazyRoutes);
+        this.done.then(() => {
+          result.resource = this.genDir;
+          result.recursive = true;
+          result.dependencies.forEach((d: any) => d.critical = false);
+          result.resolveDependencies = createResolveDependenciesFromContextMap(
+            (_: any, cb: any) => cb(null, this.lazyRoutes));
+
+          return callback(null, result);
         });
-
-        return callback(null, result);
       });
     });
 
@@ -119,7 +120,7 @@ export class NgcWebpackPlugin {
 
     // Virtual file system.
     compiler.resolvers.normal.plugin('resolve', (request: any, cb?: () => void) => {
-      // populate the file system cache with the virtual module
+      // Populate the file system cache with the virtual module.
       this.compilerHost.populateWebpackResolver(compiler.resolvers.normal);
       if (cb) {
         cb();
diff --git a/tests/e2e/tests/test/e2e.ts b/tests/e2e/tests/test/e2e.ts
index b0e49f05286d..ca66091906c7 100644
--- a/tests/e2e/tests/test/e2e.ts
+++ b/tests/e2e/tests/test/e2e.ts
@@ -17,5 +17,7 @@ export default function() {
   return expectToFail(() => ng('e2e'))
     // These should work.
     .then(() => _runServeAndE2e())
-    .then(() => _runServeAndE2e('--prod'));
+    .then(() => _runServeAndE2e('--prod'))
+    .then(() => _runServeAndE2e('--aot'))
+    .then(() => _runServeAndE2e('--aot', '--prod'));
 }