Need 4L80E Help, slips then slams 1-2 shift

This past week I did a cam swap in a 2005 Chev 2500 with 6.0 and 4L80E trans. The truck had a previous tune with HPTuners. It worked great. I wanted to use EFILive and my innovative wideband to do the new tuning, so I reflashed the truck back to stock with HPTuners so that I could start fresh. The truck shifted perfectly fine after the reflash to stock with HPTuners.
After the first flash with EFILive the trans would slip then slam the 1-2 shift. I tried reflashing it back to stock again but the problem remained. I've tried a full reflash with the stock file with EFILive but the problem is still there. What am I missing? Nothing physically has changed with the trans, just a reflash of the PCM. I've compared my stock file to another stock file from the tune repository and they're the same.
Does anyone have any suggestions? I need to get this figured out before transmission damage occurs.

Truck details are - 2005, 6.0 and 4L80E, shorty headers, no cats, dual exhaust, AEM intake, stock throttle body and MAF, and a comp cams 212/218 .568 on 115lsa camshaft.