KloveJeep

I have a 12 Jk Rubicon that has been geared and tires, and some other cool stuff done on it. The problem I have is intermittently when the key is shut off it looses the Flashcal programmer memory on it. It get stuck in limp mode when I rear start. It has been at local dealer for almost 8 months trying to figure out issue. There is New crate trans, new TCM, flashed the PCM and even charged me for a new complete wire harness. They cannot figure out and said that its because of the mods and are washing their hands with. It has worked for about 2 years with occasional issues. All anybody can tell me for sure is that it works with the programmer on it, then you turn ignition of it looses the programmer memory and it doesn't work. PLEASE help any ideas or advise would be great. I just want my Jeep back and working the way it is suppose to.