I had the same problem...I have a Logitech mouse that worked fine in every other program but GTKRadiant. After some searching, I finally found out how to get it to work:
Anytime I'm going to use GTKRadiant, I press CTRL+ALT+DEL and end the task called Em_exec...that is the Logitech software that runs in the background. You would think disabling it would make the mouse LESS functional, but it turns out I can use it in GTKRadiant now.
If you don't have a Logitech mouse, maybe you can still try it, look for a program thats not Explorer or Systray...hope that helps.