This client.wyc then should contain on 'old' version number and the path to the custom wyUpdate.exe, right?
I don't know. Double click it and see where it points to for self-updates. My guess is that the client.wyc is referencing our hosted self-update sites.
Using Fiddler I see it does not even download the wyUpdate's wys server file from the custom location.
If you're already up-to-date (your main app), then wyUpdate never bothers to check for updates to itself.
Btw: How does wyUpdate even decide if there is a new version of wyUpdate.exe, where is the 'current' version of wyUpdate.exe taken from?
Double click the client.wyc and you'll see the current self-update site. Also, see "When wyUpdate self-updates" in http://wyday.com/wybuild/help/custom-wyupdate-version.php