Re: maybe it's a midi problem?
What has helped is to send a midi at the end of each stave, as in Patch 1, Bank 0, making sure to check "Send Bank Select", then to add an MPC setting the volume to 1, and adding a single note. I tried a variety of using these singly or in pairs, instead of all three, but that did not work for me.
Interesting. That would imply that your soundcard or synthfont driver does not implement Program Changes until it receives a Note On. The problem with your fix is that if you don't play to the end of the song, it doesn't fix anything.
Your problem may be that you are starting out playing notes without an Initial Program Change or with Program Changes that do not send a Bank Select. If you could email me the file, I could investigate further. I have MIDI-OX configured to display everything that NWC2 sends. I can see exactly what state the MIDI subsystem should be in at the end of a song. This doesn't insure that your subsystem would actually be in that state, but it is a step down the road ...