Dick,
I think the problem with pickup bars or anacrusis must be a software problem, Musicator handles it perfectly, after all there is enough information in the MIDI file to get it right. The problem with Musicator is cost (it's OK if you want a sequencer, notator AND audio recording studio) but I'd be surprised if there were no cheaper programs that could get it right.

I've had the same problems with ABC programs converting between ABC and MIDI.

Cheers,
Alan