@buzz

Thanks - I finally got it figured out. I had been overlooking the files in sources.list.d/ and noticed that both collabora.list and raspi.list had wheezy listed. Changed them to jessie, re-ran the update/upgrade process and things started working - except sound. I also had to add dtparam=audio=on to my config.txt file for some reason, even though that had been fine previously without it.

Anyway, thanks again for the help working through this problem. <3 RetroPie.

@chipsnblip good point. I also decided to go carefuly this time. updated setup script, manually updated core, uninstalled all optional/main packages I don't care about. then I started update of all installed packages.

no idea what caused the problem, but now it works. update took less than 2 minutes

Having exactly the same problem!

Posted on here last week but not had a reply from anyone.

Hopefully someone will be able to help, otherwise I fear its a fresh install, which I really really want to avoid :-(