Somethings not right in your description of issues...the little fan inside the IHKA shuts off when the car goes to sleep after 16 minutes of inactivity from anything on the P-bus (door handles, locks, windows, etc). It shouldn't be the culprit of a dead battery because as long as the key isn't in the ignition and the doors opened etc. ...it should shut down after 16 minutes of inactivity. You can test this by rolling the windows down, parking in a quiet spot, and coming back AFTER 16 minutes. Don't lock the car because you will set off the interior motion sensor when you come back and lean into the car to listen to see if the little fan in the IHKA control panel is running. REMEMBER...DO NOT lift the door handle or operate any of the windows...NOR...press any of the buttons on your remote key. So basically, if you come back to the car AFTER 16 minutes and the little light is illuminated next to the gear shift lever, then the car did NOT shut down (go to sleep)....wait until that light goes off, then listen to see if the fan is still running.
A failing FSU/FSR that controls the HVAC blower will/can continue to run when the car is off and parked etc...and can drain a battery. And if you have the AUTO cliimate control IHKA panel...if the word
"AUTO" appears in the fan speed control display above the little "dashes"...the car will automatically operate the fan speed control. If you only see the "dashes" in the fan speed display...then you have it set to manual fan speed control. This could be why the speed changes and you haven't "touched" anything on the panel.
These instructions are from my e38 owners manual...but the text is the SAME in the e39:
