I am no expert so just my thoughts here, along with phone questions and info from tuner dude down here...
The bypass valve is spring loaded, make sure there are NO kinks, pinch points on the vacuum lines feeding the bypass valve.It still could be a slight diaphragm issue only under load to unload condition.
I agree there may also be small issue in the A/F table in the phase change from non-boosted to boosted operation.
(My) tuner dude says "it don't take much in that area for it to feel if it were falling on it's face for a second or two before boost comes in and WOT happens, and all is good .
The only real way to see is Dyno time and watching what the duty cycle on the injectors is doing verses what A/F ratio is saying, verses just what boost pressure is doing. per turner dude.
Did your tune also improve the Trans pressures for shifting under load? (Not my question not smart enough to ask it) Tuner dude question.
16' Heron White
#106 of 188
Whipple @ 11 psi
More fun than allowed in most states