Did a bit more digging.
A person with the same name is on the no fly list. My husband is on the "false positive" list (reminds me of a pregnancy test lol) is what they told me.
He will never get off this list but he can apply to Transportation Security (not sure what the point would be?).
What happened was: Tried online check in didn't work, tried self serve kiosk, didn't work. Told we had to go to the check in agent. When they couldn't get check in to work they had to call a special security number. They had to provide information from his drivers license, passport, how many bags he was checking and his frequent flier information (thank goodness for that....). They were then given a special "pass key" they had to type into their system and we finally got our boarding passes. Took a good 1/2 hour both leaving and returning. Desk agent kept apologizing but he did say his name was on the "no fly" list.
We were advised to show up at the airport 30-45 minutes before we normally would because we could have been denied boarding-not because of the security thing-but because we missed the boarding time.