2008 Tahoe TCM issues

Ok, have an odd one here.
A customer brought in his 1988 Blazer with a swapped 5.3 and 4l60 from a 2008 Tahoe, he was having issues with the transmission shifting up to 4th at very low mph and no kick down once in 4th.
After verifying the wiring I drove the truck and he is correct.
I then adjusted the shift points to see if it would make a change, at first it did not.
Here is where it gets really odd, I was logging during the test drive, I decided to turn off logging and bam it was holding gears and downshifting.
WTH?
I shut the engine off for 30 seconds or so to verify and it remained the same, holding and downshifting.
I let it sit for 15 minutes and tried again, it now had reverted back to low mph upshifts and no downshifts.
I drove for 20 minutes to see if it would change (all this time without the logging on) it did not, I then started the log, left it on for a couple minutes (no change in shifting), then I stopped logging and bam again it shifts like it should.

Any thoughts?

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