I have tracked the issue down to scan_sexps_forward in syntax.c
Applying this change which reverts part of  seems to fix the issue:
Alan, can you explain what the idea behind that change was?
I think it might correspond to this part of the commit message:
Reformulate code at the top of the main loop correctly to
recognize comment openers when starting in the middle of one.
: 9dcf5998935c Sun Mar 20 13:19:48 2016 +0000
"Amend parse-partial-sexp correctly to handle two character comment delimiters"