Two problems related to manual transmission have been reported for the 2008 BMW M3. The most recently reported issues are listed below.
2008 M3 dct lag problem. At lower speeds the gearbox takes to much time to select a gear (like coming through a slow corner) and then after the lag and it "catches" again there is usually a jerky acceleration. This is not normal for a transmission to drive this way. Happens more in "d" mode but also in regular mode especially in 2nd gear.
2008 BMW M3 w/dct - I was making a left hand turn and had slowed to maybe 5mph when traffic on the other side had opened enough to make the turn, I pressed on the gas and the car did nothing but continue to roll at about 5mph towards the driveway in the on-coming lanes, where there was another vehicle quickly approaching. After about 3-5 seconds of hesitation the gear engaged and I was able to accelerate into the driveway and narrowly avoid being broadsided by on-coming traffic. Had the hesitation been for any longer, traffic been moving any faster, or there being any less of a gap in traffic, I would have either of been hit, or caused the on-coming drivers to have locked up their brakes possibly causing them to be rear-ended. This transmission hesitation is incredibly unsafe and is always a cause for concern if my significant other drives the vehicle. At this point I regret not getting a standard manual where I am at least in full control of when/if the clutch engages and am in my selected gear as quickly as my arm can move. This is not the first time I have experienced this hesitation, this has been a constant issue since the original recall notice, I believe I have software version 31. 2.