I'm really sorry for the frustration. A while back I actually removed this 'feature', then put it back in after someone told me they liked how it 'fixed' a problem for them. But I guess I do see the potential for this to be a major PITA. Unfortunately I'm afraid you can't really turn it off. It should only ask you once per session, but the next time you restart your STS it will probably ask again if there's an error.
Unfortunately I have no immediate fix for you, but I will make sure this 'feature' is removed or at least easily disabled for the next release.
Thanks for your honest feedback.
Kris De Volder -- SpringSource