I first posted in the Troubleshooting category but finally i think that the problem come from the screen.
I'm using the screen in kiosk mode and full screen with epiphany, and I have some freeze if the raspberry stays up too much times.
I can control it in ssh but the screen is frozen and don't respond to my touch.
So I just reboot it and it's fine again ( if it didn't freeze at startup )
Did you already have problem of freezing ?
I read in the forum that someone have done a lot of test of booting with the display and there were not so much errors.