I've seem to have fixed the stability problems in Xgl.
I turned off screensaver and standby on the TwinView Screen, via KDE. I think the different standby and off modes (which wouldn't display in Xgl anyway) killed input. All input SEEMS to be working at this point, consistently.
Also, I have a Dual-Core processor, so I also added the following argument to my kernel parameters in GRUB:
I'm running beryl on Xgl.