Hi again, Duh, I should have noticed earlier ... the .lyx file saved by the LyX GUI (i.e., into my working directory, not the temporary directory) is *also* a complete end-to-end parse of my .tex file (i.e., has my trailing bibtex invocation, \end_document, etc). I did a diff between this file and the temporary one named "XXX" in the TEMP directory, and they are somewhat different.
Another clue as to where things are going awry?
