Thank you for your quick reply Clemens. I posted this problem up past my bedtime. When I encountered this problem, while I tried multiple things, I was kind of freaked out and was not rationally going through the obvious steps of looking at what I should have looked at. I woke up early this morning thinking about what I missed, and then I tried something that fixed 95% of the problem.
I looked at the velocity profile of the bad file in my MIDI software -- tall lines at the bottom of a piano roll view (I'm mentioning this for any beginners in MIDI) -- comparing it to the velocity profile of a normal file of a similar Chopin style piece I did on MuseNet. In the problem file, I was able to see the overall volume was much lower, and I brought the volume up on all notes, and that fixed the muted/muffled sound problem, that I was able to apply my good VST piano and it sounds good. Big relief.
There is a more subtle problem, in that the velocities of notes are identical height for long stretches, much more level at the tops than they are usually. There is some variance, but not nearly as much as there usually is on a file produced by MuseNet. Along with that, it has a mechanical evenness characteristic of MIDI rendered directly from music writing software, rather than the usual subtle variances in a human MIDI Keyboard to MIDI performance. Even though MuseNet is not using a human performance, it emulates it very well. I will mitigate it by putting in some tempo changes here and there.
In summary, I think this was failure on the MuseNet end, as it is a web interface, and I was doing something different a person probably shouldn't do, working in 10 tabs at once. That is, I had the MuseNet interface open in 10 tabs at once, working on 10 different pieces. Yet, when it came to saving the files, I was down to 2 tabs. But maybe that isn't even a good idea. My rationale for doing that is that I had a theory that as a composer, even using AI, it is better to discard compositions that are not going in a good direction, rather than trying to make the best of the direction they are going in.
Just to mention something about MuseNet for others wanting to try it, unlike some other artificial intelligence music composition tools, you can make measure-by-measure choices with MuseNet. I have generated as many as 50 measures, to choose only one measure of music among those 50, as I build a piece measure by measure. That generation time (it generates measures four at a time) can take up to two minutes, so that was my rationale of working in so many tabs also. Again, though, it was just an experiment. Working in three tabs at once means you won't have to ever wait while it is generating. I call them measures, but it generates in groups of notes, really, and number of notes is determined by the token size you choose. "Token" is a term in artificial intelligence for a piece of information, in this case, pieces of music. MuseNet works on a predictive model, predicting the next note that is most likely in a certain style you choose -- Mozart, Bach, jazz, etc. (the style choices are limited by what they offer).
Another thing about MuseNet that is almost unfathomable to any musician like myself, who in spite of my background in computers, starting programming in 1971, and I struggle to learn new music software and remember how I do various things when I don't use it for a while, MuseNet takes a few minutes to learn.