WordPress MU

Ok, I am trying to migrate my WPMU & Buddypress install to a VPS from my current shared hosting server. I migrated the DB to the new server and ran the site off the DB on the new server. Everything ran great, no problems. Then I transfered the files and pointed the domain to the new server and i get the following problem.

Some blogs work and run as you would expect, and some go to the default apache cPanel page. I am stumped as to why this would happen. At first i though it might be a problem with the wildcard domain, but according to the hosting company it is working. Then I thought maybe all the files didnt completely transfer via the FTP(havnt had a chance to confirm this).

Does anyone have any insight into why this might happen?

We are about to do the same, any solution to those problems @AnMiTh?

Check your permissions, they will most likely be very messed up.