Same exact problem here (2001 X5) and I'm using the master key. It's been happening on and off for the past 6 months. I've already replaced the battery and it didn't help a bit.

I'm taking it to a dealership near me on Monday, Jan 8. They're going to hook it up to a meter for a couple days to see where the battery drain is coming from. I'll give you an update once they tell me what the problem is.