If you leave your cell phone on in the car, it has been known to trip the alarm on E39s.
Pull out your cell and see if the problem goes away.
2001 530i/5 (E39), Topaz Blue/Stone Green/Black (118k miles) *very rare interior/exterior color combo*
2005 545i/SMG (E60), ED Order, Titanium Grey/Grey (lease over)
2014 535d (F10), ED Order Summer 2014: THIS IS THE PLAN SO FAR