Seg Swap and Shift Timing

Howdy everyone,
I have noticed something strange that I wanted to see if anyone else has noticed. First I'd like to say that I keep shift tq management active for all 4l60e tunes that I do so If you turn that off, you will not notice, or see, what I am going to be talking about. Only if you leave it active will this pop up. Also it seems to only be related to segment swapping. If you never seg swap, you will not notice or see what I am talking about.... or will be when I get to the point.

Ok, so what I have seen more than once now is this. Test drive for initial tuning notes. Everything works as it should other than the missing changes for applied mods. Modify tune to suit the mods and again everything works fine. Decide to seg swap for a tune with more flexibility or additional parameters and something weird happens. Now the shift tq management hangs for about a second after each shift is completed. Definite dwell between the time that the shift completes that the timing stays reduced before it recovers. Nothing fixies this issue. Not shift timing, pressure, adaptive table(if present), converter settings, nothing. Even zeroing shift time tables out has zero effect on the dwell time. The only 2 things that get rid of the issue are these. Flash back to original tune OS or disable any type of tq management completely.

This seems to only affect the 3rd Gen ECM. I have seen this anomaly in everything from a 99 to a 2006. Has anyone else run across this? Does anyone have any theory's on this?