Could it be an Aero vs. Basic desktop scheme issue?
I connect to assorted family machines remotely (as the "guru" who helps out when they have problems), using RealVNC. One of those machines is a new Win7 machine that runs with an Aero desktop.
Well, when I connect remotely to that machine Win7 on that machine changes its desktop presentation scheme from "Aero" to "Basic", which is fine with me. However, this display transition process seems to block RealVNC's client (and mirror driver) running on that machine from presenting the remote desktop back to me on my machine. I can see things, but nothing works... although I can seemingly move the cursor around but can't actually click on anything and have it work.
What seems to be causing the problem is that popup message at the bottom of the screen, appearing over the taskbar, which advises that "a remote connection has forced changing from Aero to Basic scheme".
All I need to do is close that remote client window on my machine, and then re-connect to the remote machine again. This time, the remote desktop is apparently still/already in "basic" presentation mode and everything now once again works perfectly with RealVNC and the mirror driver. I once again have full and complete control over the remote desktop, just in "basic" mode. I can actually see that popup message at the bottom of the screen, and then it disappears as it should.
Might this information be relevant to your "Remote Desktop Connection" story? Again... Aero vs. Basic? Does the remote Win7 machine for you also change from Aero to Basic when you connect with Remote Desktop?