Runs better with Check engine light on

[recap483]

This sounds crazy, but I have a 2010 FRTL with a 871 cummins. When you start accelerating at about 1200 rpm's it feels like you may have a clogged fuel filter.(ive changed that) When you pull a grade the check engine light comes on and the truck runs fine. When you cut the truck off and start to run again, same thing. Skips at around 12-1300 rpms check engine light will come on, and the truck runs fine. I don't have insight software, but have use a Scangauge D and got 3 codes. 254-5-0 135-11-7 and 64-0-0. anyone have an idea? Thanks