Hey Steve,
wyBuild creates patches by comparing old versions with new versions of your software. Any new files are added as full files, any files that were in old versions but are no longer in the new version are deleted, and any files that are the same are compared byte-by-byte and a delta patch is created. If you create your versions like we state in the step-by-step walkthrough then everything should work fine.
I have a few questions:
Are you creating separate versions in wyBuild? (Or, the converse of that question: you're not reusing the same version, renaming it and adding the new files?)
Is the problem really that the "catch-all" file is being downloaded, because this is a separate issue altogether? (The catch all file is an update which contains full files not patches).
Are you using any special "randomization" obfuscation on your executables? Because this will effect the patching.