I have several ideas. The first is ccleaner. It can be powerful if not set properly. Do no use it for a while. If the problem stops, post and I will tell you how I have my settings and have no problems
Actually I think I have found a fix, or at least a work-around. I was looking through my startup items in MSCONFIG and looking up the ones I didn't recognize. One of them was "KHALMNPR". It seems that this is a part of the logitech keyboard/mouse drivers and it's main function is to reset the Windows mouse sensitivity to default on reboot.
The idea is that both Windows and Setpoint have seperate sensitivity sliders and the end result is a combination of the two so by keeping the Windows one at default you only have to worry about adjusting the Setpoint slider. This works fine with my external mouse but my trackpad only seems to use the Windows slider so this resetting was a real pain. Anyway, I disabled it from startup and it seems that the problem is gone now, no more resetting.
It did put itself back into startup with a new entry shortly after I did this but since I've disabled that one as well it hasn't shown up again. Also, some people say this file is needed to make extra buttons or scrolling work on the mouse but so far I haven't noticed any loss of functionality.
Hopefully this works for you and whoever else comes across this thread.