The trans is always learning.....so after a new tune is flashed in, it takes 25-100kms of varied driving to do a gross learn and then it continually fine tunes after that.
Best to start off gently and gradually give it more gas as it learns especially if it is now boosted. The large increase in torque from a blower will also need different numbers fed to the trans to make it work sweetly.
If you are using the Whipple base map and have just modified the fuel/spark, it will still need some more work. Their tune is really basic and needs lots of reworking/rescaling and many other changes including the torque numbers.
Tables/Torque Calculation/Friction Torque Loss
Scalars/Torque Calculation/Max friction Adaptive Limits
Tuning these tables will change shift points and quality to better suit a blower.
Also, in the Whipple tunes I have seen, they turn off the Airflow and Spark Reduction to the trans but this can make the trans hang before changing as it is seeing too much torque. Re-enabling these in Scalars/Torque Management and allowing it to relearn will result in much faster,smoother shifts.
Your tuner should be able to sort this for you.