Aftermarket stereo causes anti theft to go off

So installed a new a new JVC stereo in my Chrysler
town and country. Stereo works great but it sets
off the anti theft system and then the car won't
turn on. I used a Metra wiring kit to hook up the
aftermarket stereo. Tried resetting the computer
by unhooking the battery but the car still won't turn
on. I reinstalled the OEM radio, anti theft system
turns off, and the car turns on. The only difference
I can tell is there is two wiring harnesses on the
OEM radio, a small one and a large one. The wiring
for the new radio hooks up to the large OEM
harness and leaves the small OEM harness empty.
I'm guessing the small one controls the anti theft.
Can I bypass it?