Have you checked the spare tire area in the trunk? also you may want to see if your sunroof drains are clogged or the cowl area below the windshield has leaves ect covering the drains or allowing water to seep into the car. Another thing to check is if the A/C condensate drain is cloggged.
This use to happen to me in an Rx7 Turbo a few years back, I found the clogged drain, and then let the car sit with Arm and Hammer in a box for a while to absorb the moisture.
1999 540i/6 MSport- Halos, Facelift Tails, Debadge, Maint Done
2001 740il Sport- Needs maintenance.. Parts ordered..
2006 Volvo XC90- Kid Hauler