I had the same symptom of ? marks as citations.

I had this problem with apacite.  The hack I found was to stop having
LyX invoke babel.

If I erased all the intermediate files and exprt a fresh tex file, I
found that my problem occured the last run of latex in the
latex/bibtex/latex/latex sequence.

Note: I did not have this problem with 1.1.5 and apacite with the same
lyx file.  It appeared in 1.1.6fix1

-- 
Chris

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