SP1 was the bigger headache, in my opinion, due to the Firewall issues. Like most everyone else, SP2 was a non-event for our site. Security does get ratcheted up a notch which further enforces the "don't use your Windows 2003 for surfing" policy.
Now that you have SP2, try installing the Access-based Enumeration kit. If you have a share on the server that contains folders that some people don't have access to (like the root directory for a PST Share) then the user doesn't see what they don't have the rights to read.