diff --git a/dev/openapi-ts.config.ts b/dev/openapi-ts.config.ts
--- a/dev/openapi-ts.config.ts
+++ b/dev/openapi-ts.config.ts
@@ -35,19 +35,20 @@
           // },
           path: path.resolve(
             getSpecsPath(),
-            // '3.0.x',
-            '3.1.x',
+            '3.0.x',
+            // '3.1.x',
             // 'circular.yaml',
             // 'dutchie.json',
             // 'enum-names-values.yaml',
             // 'invalid',
             // 'full.yaml',
+            'sdk-method-class-conflict.yaml',
             // 'object-property-names.yaml',
             // 'openai.yaml',
             // 'opencode.yaml',
             // 'pagination-ref.yaml',
             // 'sdk-instance.yaml',
-            'sdk-nested-classes.yaml',
+            // 'sdk-nested-classes.yaml',
             // 'string-with-format.yaml',
             // 'transformers.json',
             // 'transformers-recursive.json',
diff --git a/packages/codegen-core/src/files/file.ts b/packages/codegen-core/src/files/file.ts
--- a/packages/codegen-core/src/files/file.ts
+++ b/packages/codegen-core/src/files/file.ts
@@ -1,3 +1,5 @@
+import path from 'node:path';
+
 import type { ExportModule, ImportModule } from '../bindings';
 import { fileBrand } from '../brands';
 import { debug } from '../debug';
@@ -63,7 +65,7 @@
     this.external = input.external ?? false;
     this.id = id;
     if (input.language !== undefined) this._language = input.language;
-    this._logicalFilePath = input.logicalFilePath;
+    this._logicalFilePath = input.logicalFilePath.split(path.sep).join('/');
     if (input.name !== undefined) this._name = input.name;
     this.project = project;
   }
diff --git a/packages/codegen-core/src/files/registry.ts b/packages/codegen-core/src/files/registry.ts
--- a/packages/codegen-core/src/files/registry.ts
+++ b/packages/codegen-core/src/files/registry.ts
@@ -1,3 +1,5 @@
+import path from 'node:path';
+
 import type { IProject } from '../project/types';
 import { File } from './file';
 import type { FileKeyArgs, IFileIn, IFileRegistry } from './types';
@@ -50,6 +52,7 @@
   }
 
   private createFileKey(args: FileKeyArgs): string {
-    return `${args.external ? 'ext:' : ''}${args.logicalFilePath}${args.language ? `:${args.language}` : ''}`;
+    const logicalPath = args.logicalFilePath.split(path.sep).join('/');
+    return `${args.external ? 'ext:' : ''}${logicalPath}${args.language ? `:${args.language}` : ''}`;
   }
 }
diff --git a/packages/openapi-ts/src/ts-dsl/render/utils.ts b/packages/openapi-ts/src/ts-dsl/render/utils.ts
--- a/packages/openapi-ts/src/ts-dsl/render/utils.ts
+++ b/packages/openapi-ts/src/ts-dsl/render/utils.ts
@@ -97,9 +97,8 @@
   preferFileExtension: string;
   root: string;
 }): SortKey => {
-  const fromPath = fromFile.finalPath!;
-  const filePath = file.finalPath!;
-  let modulePath = fromPath;
+  const filePath = file.finalPath!.split(path.sep).join('/');
+  let modulePath = fromFile.finalPath!.split(path.sep).join('/');
 
   // built-ins
   // TODO: based on nodeBuiltins set
@@ -110,7 +109,7 @@
   }
 
   // outside project root
-  if (!modulePath.startsWith(root)) {
+  if (!modulePath.startsWith(root.split(path.sep).join('/'))) {
     return [1, 0, modulePath];
   }