Do make sure when they replace the regulator, they reseal the vapour seal properly within the panel. Most BMw techs, will pull off the panel, do the repair and slap the panel back on. Theres a vapour seal in there that has to be resealed. Otherwise when it rains, it will seep down the exterior window sill through your panel and into the interior. You won't notice it though... it'll just seep into the interior.
After discussing this matter with a local members on E46toronto.ca, one of them had the insight. - I was complaining of this musty smell in the interior and the rear passenger (driver side) floor was always damp. Microfilter was replaced, checked to see if the air duct underneath the driver seat was emitting excessive moisture, nobody was drinking in the car and I don't roll down my windows, rarely. Until i was enlightened with new info.
Good luck.