2005 6.0L Powerstroke losing Hypertech Tune

My 2005 F250 with a powerstroke 6.0L is currently tuned using a Hypertech max energy. I am using stage 3 and get great performance. The trouble is after about a week the truck seems to lose the tune. The performance goes back to almost stock and gas milage goes down also. If I reprogram the truck it acts like it should with stage 3 and after about a week it reverts to the sluggishness again. DTC's showing p0401 which is EGR related but I have an EGR delete on the truck. Also showing p0671 which is glow plug issue but I dont think this would effect the performance after warm.

Any suggestions? I called Hypertech and they said they have never heard of these symptoms before.