XBMC in true full screen does not allow other programs to overlay on top of it. Ya, it sucks, but no solution other than to use notification messages sent to XBMC. You can set this in the XBMC tab, of VC options, (for both Eden and Frodo). Where it says: "Use XBMC built in popup window" select "any recognized command".
Or you can set XBMC to use "non-true fullscreen". Worth a try. On some systems it works great, on others not so great. It depends on your setup.