Does it have a fuel cut-off on overrun function? Mine had the problem of stalling, mainly after stopping from speed, such as coming off the motorway with a roundabout at the end of the slip road. So I'd slow from 70 down to a standstill, dipping the clutch just before stopping. I suspect the problem is that the whole time I'm slowing, the throttle is shut and the fuel cut-off is active. Mine was set to do this at 1200 RPM and above, and I when the clutch was dipped the engine revs drop like a stone (due to no fuel). The system re-activates the fuelling at 1200 RPM, but with there being no gas between the injectors and intake valve it appears the short time before the engine RPM drops low enough to stall isn't enough for the fuelling to catch up. I could usually catch it with some heel-toe antics, but the pedal layout on the Omega is far from ideal for this and occasionally I'd get it wrong and stall it.
I adjusted it to 1800 RPM, and the problem appears to be gone. It's unlikely this is the same problem as yours, since mine is a much older system (installed in 2002) hence the reaction times are probably much worse. Certainly the mapping software is a lot less sophisticated than your system. But it's worth a look, should be easy enough to disable fuel cut-off temporarily to see if that's contributing to the problem. You lose a little fuel economy as the gas injectors are still putting in small amounts of fuel when the throttle is shut and the car is moving, but it's pretty minimal.