App_Code is not supported in a WAP. The App_Code folder is compiled at *run-time*; all code in a WAP is compiled at compile / development time. So, when you add an App_Code folder to a WAP. you end up with duplicate code; for example, a class defined in App_Code will also show up in the wap DLL. The fix is easy: just name the folder something else like Classes or CodeFiles.