P1000 code question

[axlehead]

So after debating the past few weeks over whether to flash back to stock for California emissions testing I decided to stay with the custom tune to avoid the p1000. To be on the safe side I decided to check for codes with the gryphon. Much to my disappointment I was met with a p1000 code. I was clueless as to why this could be so I flashed back to stock and have since driven nearly 500 miles mixed driving. It has been a week since I reflashed and the code is still there. Is there any chance the gryphon can cause this code just by being plugged in to retrieve codes? Thanks.