2006 Jeep Commander - heads put in wrong at the factory

2006 Jeep Commander Mileage: 14000 I just took my Jeep in after the check engine light came on & the engine started running really rough. I was told the factory put the heads on wrong. They have to pull the engine & remachine the heads. My question: Will this effect my resale value later on? I am out of my comfort zone with this problem. I know to be concerned but I don't know enough as to why I should be concerned. It is obviously still under warranty & I don't want any problems down the road. Any advice would be greatly appreciated.

Background:
Commander bought new off the lot. One year ago.
I have taken it in for every recommended service on time.
From day one it stalled for no apparent reason. The service dept. Couldn't find the problem until now.