This isn't a problem with the version numbers (or more specifically, how version numbers are stored in the *.wys file). The version numbers and changes associated with the version numbers are stored in an "offset" way for specific internal reasons. I can get into the technical details if you want, but it's not relevant to the problem you're having.
I create my patch files, and everything uploads normally. But the app won't update, it says I'm at the current version. I checked the wyserver.wys file on the server and it's showing the following:
The problem you're having is the client.wyc file installed on your user's computer has the version number embedded in it that doesn't match the version of your software. The way you solve this is to go to the "Build wyUpdate & Updates" screen in wyBuild, select the correct version number in the drop-down menu directly above the "Build wyUpdate" button. Then click the "Build wyUpdate" button.
So if you're testing updating the "3.7.390" version of your app then you should select the "3.7.390" version in the dropdown above the "Build wyUpdate" button. Then include the client.wyc and wyUpdate.exe with your app.
Does that make sense?
EDIT: Also, it looks like you're hosting the updates / server files on 3 separate sites. Make sure you upload the *.wyu and *.wys files to all the sites. That is, make sure they always have the latest version.