Hi Robert, I know this is like computer phone support asking you if the modem is plugged in and turned out, but are you using barchecks on every bar? Saves a multitude of problems.
May I make the polite suggestion that it is very often, in my experience, the act of making an MWE, even if difficult, that many times resolves the problem for you? Or at least a binary chop approach?
You could mail me the score if it is not secret and I will look at it for you also.