There are no issues on our part. We integrate with vbportal 3.0 and Vbulletin 3 just fine
http://www.reeftalk.com/gallery/index.php
In fact vbportal integration is quite automatic.
Couple thoughts here. If your using some custom vbstylesheet how is there path's our issue? If they use relative paths they need to be full urls. People seem to miss that html lesson. If your trying to load images or header over some other page your url's and images have to be full url not relative links or they will not be found. I consider this one of the biggest buggiest things about vbulletin. They use relative paths consistently. It would be so easy for them to prepend the bburl on the wrong of all paths but they do not.
If you link a url for us to see we might be able to give some suggestions