I can cautiously say it looks like the issue has been in fact as suspected: unclean, "no clean" flux.
The previous units that I reported as "working," but not working with buttons as expected - this was user error. I didn't think about the fact that since faders were not connected, there were floating pins, which of course threw off button behavior. After thorough cleaning and connecting faders to floating pins, I have two completely working units now, that were previously defunct, and a third brand new one - a new Teensy installed in an previous carrier main board, working.
I suspect I can reinstall two more removed Teensys and at least one may work fine; I will try.
One carrier board and Teensy appear unsalvalgable and behave strangely no matter how clean I get them.
Also, in other news, I am now getting failures in the field, customers returning units behaving bizarrely, the strange behavior showing up after a few hours of use. Of course they were thoroughly tested before I shipped them.
Dirty boards is the only explanation I can come up with, as the designs are tested and I have units working for years without issue. Software is well tested and again, working for years without issue.
Why some boards have worked and tested fine, then failed in the field, I cannot say - humidity? Heat from the unit spreading the flux further? I don't know
This has been a very terrible and expensive lesson in flux. I have processed and used at least 100 Teensys in a similar manner, leaving the "no clean" flux on the board and I've had no problems at all - until now. This was a new flux, a "freebie" I got with new 63/37, and I'll never do that again. On closer inspection, it didn't actually say "no clean." It said everything else - neutral PH 7, non-corrosion, etc:
I am also leery of using the solder from the same company now, since it contains the same flux:
I'd rather bin it than have more failures, as this is getting expensive and humiliating.
I am not 100% feeling good about all this yet, but after some thorough testing I will post more...It's been incredibly stressful as I sell units to customers and now some are failing. But at least I think I know why, and how to fix the issue.
Thank you again everyone. I appreciate the immense support. I'm sorry to bother you all with such a stupid final problem as dirty boards. What a joke. I just didn't know any better. Until now.
I will post further again after thoroughly testing the units, as well after receiving the USB sniffer Paul recommended. I am hopeful that this is, indeed, the end of the issue.
All the best,
Mike
EDIT: after all this, I thought you might like to see one of the products I make with the Teensys: