I have this same issue... MacPro3,1, OS X 10.6.3, 64 bit kernel, Virus TI Keyboard.
The problem is really annoying for me, as my Mac Pro is always on (doing protein folding). To avoid this issue I would have to power up the virus, and never power it down, or be forced to restart the whole process... Pause folding - power down mac - power up virus - power up mac - restart folding... I know I could just stop folding, but I'm really into it... 
Any news on the subject?