Okay I think I may have a resolution for you. With the category option.
I was able to duplicate your problem.
Try this in the control panel.
Control Panel » General
Expand Forum Summary Options
Deselect Enable Categories?
It appears that you may have had a category existing and the upgrade may have enabled the above setting.
If the four forums are not assigned a category they will not appear if the item above is enabled.

Blue Man Group
There is no such thing as stupid questions. Just stupid answers