Hrm... I can't reply via another comment because my reply was too long. This seems to me a bad design, as it disrupts the "reply" threads. Oh, well...
Anyways, Ctrl-alt-F1/F2/F3/F4 etc. are captured at a VERY low level; outside X-Windows and Gnome altogether. While there are many explanations of these keys and how they work, this one seems quite readable:
http://linux.about.com/od/linux101/l/blnewbie5_1.htm
While I can see the value in begin able to pass these keystrokes through, I also see the importance of ensuring they always work locally. If there IS a way to do this, it would have to be implemented on your client RDP program - i.e. when app has "focus", disabling all the Ctrl-Alt-F{n} keys and forwarding those to the remote machine, and when the app loses "focus" restoring all the Ctrl-Alt-F{n} mappings so they work properly for all other applications and from the Xwindow system itself.
Dunno how that might work at the moment; I'll keep my eyes open for solutions and let you know if I find one.