Thank you both for helping. Much appreciated.
Both computers share a library. The office is the main computer and the home theater is the client. I do most of my work (editing, creating playlists and particles) on my office PC. It's my understanding that properly downmixing to stereo is possible when the multichannel track has the downmix coding (I could be wrong) and not all tracks have this. But either way, I don't do critical listening in my office, so this isn't that important, just something that would be nice. The JRiver downmixing is sufficient for my purposes.
To test further, I used mkvtoolnix on an mkv file which I had already created particles and changed the default track to multichannel. I then replaced the new file with the old file (same name and directory). I played 3 different particles and they all defaulted to multichannel, but then, all of a sudden, I got the dreaded particles of death! The particles had renamed themselves and became un-playable. This is a strange known issue with particles when they change names/folders randomly, but it usually happens when creating them. This was the first time it happened after creation. I can only presume it had something to do with replacing the main file with the changed audio default.
RoderickGI, thank you for pointing out the "Playback Info" field. So far, this seems like the best option. I tested this on one particle of an mkv and I was able to copy/past it to all the other tracks. Seems to work well. Much easier than going through 35 different tracks and changing the streams. Also easier than using mkvtoolnix to change audio track defaults on over 150 very large mkv files.
Thank you both for all the help! Much appreciated.