Well, wyBuild doesn't treat obfuscated files in any special way. It just dumbly scans the differences between files (no matter what the type) and generates the smallest possible patch.
If you flip between version 2.0.3 and 2.0.4 versions of your software is the local path the same?:
[attachment=0]patch-example.png[/attachment]
Because they should be different.
Also, the version number is stored in the "client.wyc" file. It doesn't read your files an try to parse version numbers from that. That is, if you tested updating your app once with the client.wyc file, the file was updated with version 2.0.4. So subsequent runs of wyUpdate will say that your app is up-tp-date even if you have the 2.0.3 files.
Long story short: click "Build wyUpdate" to rebuild client.wyc for version 2.0.3 of your app.
Tell me if this helps.