Since it's in Remote Desktop, maybe try setting Apply Windows key combinations to On the local computer (expand Options in Remote Desktop Connections then go to Local Resources tab). That would tell you where the extra keys are being "added," at least.
Does it happen all the time or just sometimes? Also, have you tried rebooting the remote computer?
I run into this from time to time on local PCs (never in Remote Desktop, though). I think I finally figured out that closing one of my programs (PSPad) fixes it. Can't remember for sure.
I've Googled around about this before, but I've never been able to find a definitive cause or solution. Have heard of people hitting ESC, ALT, CTRL, CTRL-ALT, etc, several times to fix it, but can't confirm that.