A while ago I had a unusual problem when I did a similar thing on my cftbl. When you lift the playfield and put it back in the plunger rod comes very close to the ball eject solunoid that shoots the ball back up to the playfield into the right lane. I broke the wire connector off the solunoid base but not the wire to the solenoid still worked but knocked out the GI lighting because of the bracket it was shorting out to. It could be a similar thing but touching something else - worth checking.
