veetid... I have been having the same exact problem... the difference with my setup is I am using a 3.5" HD. Last I read on the board the talk was that the power to a 3.5" HD was likely the problem... I am in the process of converting to a 2.5" to see if this solves the problem.
Now the other things I have suspected is a USB conflict with the GPS... mine seems to reboot more often when the GPS in running... Perhaps there is a driver issue between my touchscreen usb driver and gps usb driver? (I use a Xenarc Screen)... What sort of screen are you using?
Anyone who can weight in... please do... I am in need of a solution too. Thanks.