I just did this also and had a whole SLEW of problems.
The version just would NOT update AT ALL. I filed a trouble ticket and was given this:
Try the following and let me know the results. Essentially there looks to be an error in the version checking step of the upgrade. This URL will skip that step and move on to the next step.
Change the URL as follows adding "?step=4" at the end.
http://yourdomain.com/ubbthreads/install/upgrade.php?step=4~~~~~~~~~~~~~~~~~~~~~
After doing that, I STILL had serious problems including links that want to download, instead of opening a page and other pages being brought up as 'blank'.
Again, trouble ticket worked though them, but STILL things aren't right, or at least don't FEEL right (if that makes sense)