there have been a few issues with pulsating throttle, etc on these cars. I myself had mine reflashed (not under any service bullitin, although bmw did pick up the cost) several months ago because of a pulsating throttle issue i was having. Mine is a 2.5 so there is obviously some differences there, but in my research on my particular problem i came accross a few 3.0's with the same/similar issues.
For Example:
http://forums.bimmerforums.com/forum...d.php?t=778912
http://forums.bimmerforums.com/forum...d.php?t=785703
http://forums.bimmerforums.com/forum...d.php?t=787708
Post something up if you can get any info as to what it corrects. The more that's online the better.