This sounds exactly like the problem I reported not so long ago. It only happens occasionally and I have yet to spot any pattern or discover a means of reproducing. It has also been around for a while (by which I mean at least 6 months, probably longer) and I actually meant to report it long before I did. I now habitually run sync twice, as described by the OP, for safety. The problem occurs maybe one in twenty times.
Regards, AB