Been noticing this on 6th gens as well... What I've noticed is the timing is pulled out after each shift for approx 1 second(ish) too. It's there on stock cars, but more noticeable on cars with more mods done to them.
Here's what the timing looks like after each shift (retarded -then flat as commanded)...
tm-shifts2.JPG
It almost feels like some kind of clutch protection TM, or similar. I asked HpT if we might be missing any tables related to this, but was told that everything was mapped out.
Not sure if this is what you might be feeling too...