RX300inSC

My RX was broken into this week and the thief broke out my rear, passenger side window to get in the car. Insurance is paying for the repair but after installing, while rolling the window up on Auto it goes up then back down halfway. I am sure it is because the computer, motor and window all need to be reset because the computer does not know where the window is at right now and thinks it is pinching something. Does anybody have any advice on how to correct or am I making a trip to the dealer to have the computer reset? The installation tech has already tried twice with no success. Oh just in case anybody was wondering, they stole my Garmin Nuvi.