[avishenoy1]

Definitely sounds like a tune issue. The transmission ECU has set speed limits for shifting in each gear which can be found in the factory service manual. The 4.88 FD messes with these by decreasing max speed in lower gears.

Its likely more of an issue between 1-3 as the percent change in speed over the stock set point is greater than in 4-6. Edit: (I think, but not positive.)

I've read that this will only affect the gear number shown on the dash but it seems to me like it's also affecting the tcu logic as well. Try going back to the stock tune just to see if it changes anything. Pretty sure you can solve this issue with an ECUtek tune as well.