The catch-all update is downloaded when a file fails to patch. That is, either the file was modified by the user or the file just isn't what wyUpdate expects it to be (based on what you used in your wyBuild project file).
To find out which file is failing, in wyBuild go to File -> Properties -> Update & server files then uncheck "Create a catch-all update for corrupt installations". Then rebuild & re-upload your updates.
Then, when the update is installed, you'll see exactly which file fails to patch.