That's what I was looking for. In the other threads about this problem everyone was trying to figure out what they might have done wrong. If you're sure that it never worked right in 2009 then it shipped with this problem.
Do you have the original 2009 clearance file? Since you haven't switched from 11 yet, can you compare the two files?
You might be able to use the 11 file, but you might not. 2009 may require something new, for example, at some point they added something new to the thread file (cell a1 needed some special code or something) and people who had modified their's couldn't just copy it.
I wish someone from Autodesk would weigh in on this issue. Have you been watching the other threads to see if there has been any sort of resolution?