Does the wyUpdate window show and does it "do something"? That is, has the update process taken place?
Also, did you follow the step-by-step walkthrough
? This covers everything you need to know in an easy to follow way. Don't skip any steps.
My guess is either you're not including the correct files in wyBuild (make sure you include [*]all files[*] for [*]all versions[*] in the version tabs in wyBuild). Also, make sure you're not getting any warning in wyBuild when you build your updates.
Lastly, double click the client.wyc file in the folder you're using to test your app. Does the version in the client.wyc file match the version of your software?