I see 90Ah rating for the OEM M3 battery an 55 Ah for the CSL/Mini battery so you're still dealing with nearly half the capacity on the battery. I'm not surprised at all that there are still issues. The capacity determines what kind of reserve time you'll get out of the battery which is directly related to how long it will last between starts. Since there is always a small draw on the battery even when the car is off, that reserve capacity is important unless the car is driven daily or its put on a trickle charge when not in use.
09 E90 M3 - Interlagos Blue / Black Novillo / Sycamore Anthracite / Eibach / HRE