Windows keep going in and out of focus on remote desktop

So I keep having this problem when connected to a remote computer.

(Both systems running Win7 64bit OS)

The windows on the remote computer keep going into and out of focus.

Everytime I try to click on a minimized window in the taskbar, the prompt pops up briefly, then goes away.  It's the same way if I try to rename a file on the desktop for example.  It highlights the text for a second, then by the time I type something I can no longer edit the text.

I've tried changing the speed/quality setting but it doesn't seem to affect it.

I'm stuck.  Does anyone have any idea how to fix this?