I like how this thread is unattended. I actually may have the solution, sorry for being late.
I also had a BMW 528i E39 1999 year model. (original buyers and parents say its 2000) The problem started when the battery was always dead, I replaced the battery; after a few weeks the problem persisted.
I found out from my local mechanic that it was a defective unit in the A/C Fan unit. Don't believe me?
Once you jump start your car and verify that your battery is working efficiently (go to a auto store and tell them to test your battery, say you have it warranted if you don't.) They will test if the battery can hold the charge. Turn your Fan to the middle setting, than to full blast. There will be no difference. The fan system will also run even when you remove the key. If these factors are faced by you, there is something wrong with the fan. The repairs on my E39 was over 400 for parts and labor.
The reason why your battery is dead on a regular basis is that the system runs even when you are not at your car. When the car is off, the alternator is not creating energy for your battery.
Last edited by Pwnography; 08-29-2012 at 07:55 PM.