are your songs quite busy? Are there lots of midi notes and a lot of CC activity being sent at the same time? Hardware synths have finite polyphony, and it is possible to send more notes and CC data than they can handle (at which time, stuff starts falling through the cracks)

I don't know if soft synths have the same polyphony issues or not. On my Roland hard synth, one guaranteed way to drop notes is to add lots of individual CC volume faders to multiple MIDI tracks. CC data can easily double or triple the amount of info the synth has to handle.