I have the same issue, very frustrating. Using a Win 2003 AD and 10.8.2 server and clients. If i use WGM I can see all users and groups correctly, but Server.app and Profile Manager does not show them correct.
Strange that we see issues like this since Profile Manager has been around for a while, really interested to hear other peoples experiences.
PS I see a similar thing here: https://discussions.apple.com/thread/4417085?start=0&tstart=0