Well, if you followed everyone's instructions/advice about upgrading to vBulletin 4, you probably wouldn't have had any problems. We have mentioned in NUMEROUS threads that most if not all modifications and styles will NOT work with vBulletin 4 and you should disable and/or uninstall them prior to upgrading (including deleting the files associated with the modifications).
I had 20-something modifications on my site, and upgraded just fine
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