Hello Lorna,
We have two E46's one a 320Ci the other a 330Ci (VDO/Siemens MS43 ECM's) they both occationally do this. I have found that if you remove the key from the ignition, open and close the drivers door, no need to get out, lock using the remote, wait 10, or so seconds, unlock and the try again it clears the problem every time.
I have also found it happens more often if you jump in and quickly go to start the car, which would make me think it's a "comms" issue. Being lazy in my old age, & because I have a fix, I have never bothered to investigate any further.
My commuting vehicle is a 2009 Merc 220Cdi with 270K on the clock, this also does the very same thing too, but worse (can take several attemps to get it to clear & start) and more often than the E46's.
We previously had a E39 525D (Bosch EDC 15C4 ECM) and this happened with that too.
If you haven't already tried the Lock/Unlock method, give that a go.
Alan.