Hi Johan,
I tried recreating the problem here but it worked fine for me. Here is what I did:
1. Inserted a Violins I preset in the score
2. Clicked on Violins I and hit Shift+I to bring up the Shift Instrument Dialog
3. Clicked on the New Instrument button
4. Chose a Flute and hit OK
5. Back in the Shift Instrument dialog I selected Voice 2 for the flute and l;eft it on default channel and hit OK
Both instruments were playing correctly - the violins were triggered on voice 1 and voice 2 triggered flute notes.
Are you not getting the same result if you follow the steps above?
Lubo Astinov