Data Transfer brain fart between Server 2003 boxes

I have a client who is replacing an old server. We have installed the OS and copied the files accross but now we're getting permission issues accross the board when it comes to opening or saving files.

What am I missing, is there a specific copy switch or method I should have used, I have tried using synchtoy to keep the copies synchronised before switching people over and that was working ok, I have also tried manually copying specific folders between servers and yet the same permission errors come up.

Is it an active directory thing perhaps?

I'm sure its something fairly obvious and the solution lies in my brains equivalent to the "tip of my toungue" but I cant remember for the life of me what it is.