I upgraded to 9 from 8 over the weekend and am now in the process of finding my way around it. I've read with dismay that Categories now show in a non-hierarchical manner (i.e. not under their folders) in the category pane, but that is only part of my problem.
The dump (which is only how I can describe how it appears) of categories in my category pane is also:
1) not complete; some catgories only show under their parent entry and some seem not to be showing at all. What shows seems quite random.
2) I get random semi-colons on some category names that don't show when i go into the category folder
3) some categories show in different sized fonts
Is this likely to be a result of bad conversion of the data from 8? It all seems there and in working order in the categories folder