Though the govt. is sketchy on details, they indicate that there has been a massive expansion of the no-fly list over the past few months. There's no reason to believe the "automatic selectee" list hasn't grown a bunch too.
Just over the past few months, we've had the Cat Stevens incident (which was international so technically in a different system from the CAPPS/SSSS system), Sen. Ted Kennedy denied boarding for several weeks until he personally called Tom Ridge, and some vague stories about Rep. John Lewis either being SSSS'd on every trip or denied boarding depending on how you read it. There's no reason to assume that thousands of innocent non-celebrity Americans aren't being caught up too. Personally I fear a sudden run-in with the no-fly list every time I go to the airport.
If it keeps happening (for non criteria tickets as you describe), you should seriously consider complaining to UA (assuming all three on UA), the TSA ombudsman, and your Congressman, and
cc: all of them on each other's letters. Explain to your congressman how this is disrupting your business/life. Explain to UA how it is disrupting your travel and you are considering switching 100% to AA. Maybe send a copy of your AA elite card.
Tell UA you won't accept any BS about "safety/security" in their response. If you're real ambitious, tell TSA you are looking into hiring a lawyer and do so. You have little hope of getting it fixed, but those are the best "official" routes.
You should also try and see if it happens on AA too. If both, it's a better indication your name is being flagged.
If no luck elsewhere, consider slight alterations of your name on your tickets and/or FF account. (On UA, you can apparently "change your name" on the FF account with no human intervention. ) If your name/ID is (and you normally fly as) "John Q Public," try "J Q Public," "J Quincy Public," or even "Public John."
Good luck. If you succeed (or fail), it would be nice to hear about it back here on FT. I fear more and more of us will face this problem as the government moves towards its grand goal of a single/unified/huge no-transport list.