This is a slightly unusual situation. I have a MOSS 2007 farm. I do a database backup and restore to our dev farm and then do a database attach to our 2010 farm.
I'm secondary site collection secondary admin on all the site collections in the MOSS farm, and if I go to Central Admin on the 2010 farm, I'm still secondary site collection admin, according to CA. However if I navigate to the site I get permission denied. The fix is to go through central admin>Site Collection Adminsitrators and hit OK on each page, which seems a bit odd for me.
I've tried assigning myself site collection admin in powershell and, although I can change who's listed as the site collection admins, it has no effect until I go into Central Admin and hit OK.
Which is all a bit confusing, have I missed something?