Thanks Jason! I will follow up on your suggestions. One thing I do a lot is move things around from instrument to instrument. I might for example copy/cut/paste, or physically move, a viola passage and put it on the second violins. I notice that when I do that, the midi channel listed cin Sonar's event list will have the wrong channel, in this case the viola channel instead of the sceond violin channel. I have always assumed this did not matter; there doesn't seem to be any quick way to change it, other than changing each note individually.
I will go on a search foe any possible events on other channels that could be interfering. I'll let you know how it goes.