Except when I disable the Navigation Pane. Then the mouse becomes as responsive as I would normally expect. I thought it might have to do with the RDP connection I was using running RDesktop from a Linux-based thin client, but when I use a Remote Desktop Connection from a W2K8R2SP1 server, I see the same behavior. This is really annoying.

Changing the theme from Windows 7 Basic to Windows Classic did the trick. The issue is created by the fade animation used by the Basic theme when moving the cursor in and out of the navigation pane. Alternatively, changing the performance options by un-checking "Use visual styles on windows and buttons" works as well.

Sounds like Explorer is trying to scan drives - if you don't need them make sure your RDP client is not set to map your local drive resources - this will cause that kind of behaviour. You need to change / save the RDP client options to untick drives from local resources.