I have a CLK320 and have a similar problem. However, I think I isolated the sequence that makes it happen. The trick is to lock the doors BEFORE you shut the passenger door.
1. Unlock the doors using the remote.
2. Open the passenger door.
3. Lock the doors using the remote.
4. Shut the passenger door (usually works better when all windows are closed).
5. Unlock the doors using the remote.
6. Pull the passenger door handle. It usually will take two tries to open the door.
I spoke to my dealer about it and he is checking with MB. He has tried to fix it for another customer but has had no luck. I plan to wait for a service bulletin.