I have a Domain Admin User that logs on via RDP to a w2k8 r2 server, UAC is turned off locally at that server.
Whenever I try to access certain folders, I'm getting the following prompt: "You don't currently have permission to access this folder". When I try to launch certain programs, I have to right-click "Run as Administrator" to gain admin elevation and e.g. write rights to the program files folder.
When the very same user logs on to another ws2k8 r2 server, I don't have these issues. Both servers a freshly installed.
When you check "Effective Permissions" on the folder against the logged in user, do they have the permissions you expect? It is possible to remove permissions from the domain admin account(s). You could assume ownership and reset the permissions, but it might just be that the user account you are using simply is missing from the ACL (or has a deny in there for some reason).