I am sure if you go to Autozone to scan the code its going to come up P0600 Serial Communications Link. I have been having this issue on and off now for about a year. I can make mine do it by shutting it down and restarting within one minute. It usually happens when I stop for a drink at the local convenience store. Occasionally it will just come on at highway speed for a few minutes then go out again. Like you my battery was completely drained once, so maybe we are on to something.

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Dennis
2006 E320 CDI Black/Black Leather. Nav, HTD Seats HK stereo 32000 miles.
2000 VW Passat 1.8t 300,000 miles as of Dec 09, 2009 original owner
1997 E300d Silver 300,000 miles As of Jan 05, 2010
3rd owner SOLD