There was (is?) a bug that somtimes does not put you on the upgrade list when you use Fly Now. I discovered this on a trip one time when I was not upgraded even though the plane pulled back with half of first empty. I checked on arrival at MSP with a CSR and found that I had not been placed on the upgrade list, even though I was eligible, of course. And I had been placed on the list for the second leg. The first leg did not "take."

lately, I have had no issues, so it might be fixed. I would check to make sure you were not left off the second leg.