Wow. I'm having the same problem. I just purchased a Certified/Pre-Owned 2000 528i at 59k miles about three weeks ago. Noticed it when I test drove it. Made a note to the salesperson. She is excellent by the way. She sold the car when it was new and took care of the owner everytime there was a maintenance to be done. THe car had detailed maintenance records. Car looked like it had hardly been used. No wear and tear on the interior or exterior at all. Anyway, when I first turn the car on, it sits at 750RPMs. Then after three minutes, the RPMs dip to 500 and the engines shakes as if it's about to stall. Then it "recovers." But ten seconds later, it dips back down to 500RPMs again, almost stalls, then recovers. It does this every ten seconds. But after I drive it for a while and sit at a red light or whatever, it runs smoothly. I sent the salseperson an email and they are going to take care of it. It's still under warrenty which is cool.
If you're in the DC area and would like a real nice salseperson to talk to about a new or used car, ask for Nan Wong. Nicest salesperson I ever met and will bend over backwards for you. She's been there for 13 years. I guess that says something about her service.