I just noticed in TouchKit that it is showing my main monitor as Monitor 2. It was Monitor 1 before I disconnected the touchscreen.
I have a 4870x2 video card, which shows up in Windows as 3 monitors with two disabled. And the touchscreen shows up as number 3 for some reason.
I'm guessing this has something to do with it working now. And I am running version 5.0.1.5310 of the TouchKit x64 Drivers.
So, I'm hoping that next time I reformat and have to install this again, I remember to install everything, then disconnect the touchscreen and boot the pc without it for a while, then reconnect it and hope that fixes it. Arrg....