I just got a message from the auto-updates for scripts, the message box popped up before signing in. After updating, it asked to restart messenger (fairly normal). I think there were 4 that updated. Of those 4, 3 of them I had disabled previously.
After I signed in, I noticed that the scripts are now running. Looking in scripts preferences, they are still unchecked, but running anyway.
I know I'm not running the latest version, so not sure if it was fixed or not.
Windows XP Service Pack 3 (5.1.2600)
Windows Live Messenger 8.5.1018
Messenger Plus! Live 4.80.0.356