I do not have a remote starter, but I am having the same kind of touchscreen problems. I have narrowed the cause down to the volume control on my unit. Every time I move the volume up/down doesnt matter, I lose control of the touchscreen.
The only way to get it back is to press the map or menu key then it works again, until I move the volume of course.
Does this sound similar to your problems?
I never had the problem before doing some mods (probably a coincidence) but I have a PAC audio module connected and my last test is to disconnect it; I have been working with Pioneer and if that doesnt work they will deem it defective and have told me to send it in. You may want to call them and start a case to document everything you are doing to solve it. I have heard some horror stories about Pioneer not accepting some units.
I havent gotten around to disconnecting the PAC because at the moment I am sick of taking my dash apart for this thing.