This has only occurred in 4.0.0.0 and I've just now installed 4.0.0.1 so I don't know if it still applies. But when PatchMyPC self updated from the 3.x series to the 4.0 series it didn't carry along the "DO NOT UPDATE" settings from 3.x. The upshot of this is that it uninstalled my MalwareBytes Corporate 1.80.x program and license and installed the Home Premium 3.x unlicensed version. This is a VERY bad thing. Hopefully this error has been or will get fixed quickly.
This is still happening with v4.0.0.2
Sorry, the format has changed please right click the apps you want to always skip and use the context menu to disable the app from updating.