So you're saying that when a new version becomes available of an application that is disabled through Catalogs or Access Control, that it becomes re-enabled? We'll check into that and publish a fix if that's the case.
I've confirmed a bug that occurs when Installatron downloads new versions of disabled applications. Instead of automatically disabling the new version(s), the new version(s) are enabled based off the server's Dependency settings. Any old versions that were disabled stay disabled though.
We will issue a patch for this later today. I'll post again when the fix is available.