You need to uninstall and reinstall at least. I have not had this problem in a while and I do use the open on startup. I believe it has more to do with what you are trying to do in UL than it just happening because of the Open on start up setting. Both times I have caused this it was messing with today plugins within UL one was what I described about 5 posts up and the other I was messing around trying to customize the SBP PP plugin and screwed up the ini file somehow.
If you have a safe mode installed (such as SBP PP) then you can boot into safemode and uninstall and reinstall OR if you have a back up of your ini you can replace your ini from the backup and it will fix your UL install.
I would advise anyone using UL to get sprite or another backup program as well as a safemode program. Once you get UL the way you like it and stop tinkering (i know its hard
) then you should not get this issue anymore.