I saw something similar, I just installed Vista 5278.. After I logged into the domain for the first time, all my menu's started flickering... The active windows no matter what it was, would flicker..
I popped up the Taskmanager only to realize that the system was using aroung 97% CPU at all times, but no applications in the list were really using anything. Then I noticed that wkix32.exe was running, and was using around 8 % CPU time, in my domain we run a small Kixtart gui login, when I killed that process the system went down to using around 5-10% CPU and the flickering stopped.
So add Kixtart to applications that will make vista behave funny :)
PS is using kixforms for the GUI.