Has anyone had the issue where a sub category is aligning to the right? We just upgraded from 2006.8 to 2009.1 and are now seeing this issue in some sub categories
Yes, it does that. There isn't a fix for it yet, not sure if SP2 has it fixed. I expect that v10 won't have that issue, but I don't know.
We filed a defect for it on the same day that v9 came out, and it still isn't fixed.
If you have an even number of subcategories, then it should look ok.