Got a strange situation here and I don't know what to make of it.

I got a 4l60e that is stack shifting (1st to 4th shifts early, and doesn't drop down at deceleration).

Put it on the computer, logged in and verified. When logged out, the transmission started shifting properly.

Turned of truck, let it sit, and restarted. It was again stack shifting. Logged back in again - stack shifting continued, then logged out and it once again shifted normally. Repeat process, etc.

Asked HP Tuners what this could be and they thought it was either bad TCM or wire harness.

Any thoughts or ideas? Other trouble shooting besides buying a TCM and flashing to test?