Turn the boost overlay on and check to see that you're hitting 12.5 psi, stock is ~9. You won't feel a huge difference between 3.5psi, but the power is definitely there. I had the same misgivings as you did when I first got it installed, I wasn't sure whether I gained much at all. After doing a few pulls through 2nd/3rd and then driving the car the next morning (oil cold, JB4 deactivated) I noticed the difference in power.
2011 335i sedan 6MT, JB4 w/FlexFuel wires, AA 4" DP, VRSF 7" FMIC, AA turbo-back exhaust, ST Coilovers, BMS Intake, UUC DSSR+SSK, ER CP, BMS CDV, BMS OCC, Arkym CF trunk