I think I've found the cause of my problem and it doesn't seem to be related to a particular ST2 version. Apparently, uninstalling the SODA theme from Package Manager causes all sorts of bad things to happen in my setup. I reverted to my "old" version and it was still messed up. Reinstalling the SODA theme fixed everything.
Now however, it seems I'm stuck with the SODA install. I no longer use/need the SODA theme so I don't want it installed but uninstalling it or even deactivating it causes all sorts of problem with my GUI.