I have a 2001 325CI convertable that the windows won't always drop down nor go up when you open and close the door. Sometimes when you close the door you have to reopen in to let the window drop down then shut it again to let the window raise and seal against the top. It's like the car doesn't know when the door is open or shut.

SOURCE: convertible top won't go down on my 1998 bmw 323ic

Sounds like the sensor has faulted or the pump has become disengaged. Usually when the light is flashing it's a sensor. You can check for a pinched line or low fluid also. There is a manual lock overide procedure to get the windows up, it's in you owners manual.
Good luck...i hope this helps,

SOURCE: 2003 BMW 330CI convertible frt. passenger window does not retract

the problem is in the door lock and the assemble must be changed. when one looks in the catch which look the door you will see a white switch in the lock and this the defect. the switch is built in the lock.

SOURCE: 2002 BMW 325CI (convertible)power window

My window on my vert was doing that. Short of opening up the door and trying to do it myself, I took it in to the BMW guys at Bimmerhaus. They readjusted the window for me and it was good to go. Pretty much cost 1 hour of labor and a couple of clamps. $100+ or thereabouts.

SOURCE: Hello, I have a 1994 325i convertible. The driver

Have dealer look at it, it's a programming issue w/ECU.

SOURCE: When I close the door on my e36 325i convertable

Hi,
You have a problem in the window regulator assembly.
Go to a nearest garage and have check the window regulator, sounds like the gear mechanism have been nicked and releasing the window in heavy vibration.
Hope that helps!