Thanks for all the reply's. I also stopped by the local dealer to get some wheel spray, and locking wheel lugs (can't believe the car didn't have any), and we discussed the problem as well.
His answer was that he remembers a lot of the E39's having the motion sensor go faulty and become hyper sensitive or intermittently give off a bad alarm. He stated they used to replace a lot of them.
I am having them go over the car next week as a preventative measure, to find anything that may be in need of replacement or things that are ok, but I should keep an eye on and will ask him to check the battery too. (I'm sure this is akin to giving them a blank check, but I'm still interested to hear what they find.)
I figured it was late night paranoia, but when I finally own one of my few dream cars (Lotus Esprit, Ferrari 308, and Porche 911 late 80's version are my other dream cars) I've become awfully protective of it. LOL