Rough idle when cold

why does my 2015 Jeep Wrangler JK 3.6 have a small rough idol when cold, and it's enough to make themcheck engine lite come on?, I just did major work to it, intake cam, injectors, plugs, coil packs, new harmonic balancer, new radiator etc. It runs great but sometimes in the morning when it's cold it idols a little rough untill it warms up. I had it checked at a shop with a $10,000 scan tool and everything is working correctly. When the cam took a crap it stored a code for cyl. #5, (the cyl. that had the problem) and now it runs perfect but when I check it with the sacn tool it says it has a perm. code for cyl. #5, so I'm wondering if the computer has that code stored in it and that's the occasional problem. The lite goes on for a few days and then goes out for like two weeks, and I did clean the throttle body, I'm stumped, thanks