Have you had your intake valves cleaned? I wasn't seeing misfire codes, but was getting small "hiccups" -- and occasionally larger ones that really felt like misfires, but no codes being thrown -- with Cobb installed, running Stage 1 Aggressive + FMIC (mine also diminished or went away when Cobb was uninstalled). Had intake valves cleaned in December and the issue has not resurfaced. Coincidentally, cyls 4 and 6 were the nastiest looking IIRC.
Also, if you want to confirm a bad coil, reinstall your Cobb and swap coils on 4 & 6 with 3 & 5. If the misfire codes pop up on 3 & 5, there's your answer.
2008 E90 335i // Black Everything // photos
COBB tuned / QTP e-cutouts / Helix FMIC / cp-e DCI / AWE BOVs / Black M6 wheels + Toyo Proxes
(and yes, I am a girl)