Listen to Josh, he is a smart guy when it comes to tuning.
I was have the same problems with bogs on 3rd shift (6AT) and he tuned it right out. Took a couple tries with different maps, but I have a VERY strong car to show for it now.
You probably need to raise your OL Fuel table significantly like josh did for me, but it all worked out.
2009 e90 LCI Blacked Out Space Gray - Vishnu Procede 2.5 w/9-10 Aggressive Map Stg2 - PWM Meth (80%) - BMS DCI - VRSF Intercooler - VRSF Downpipes - HKS Cat-back Exhaust