I Always Feel Like Somebody’s Watching Me

Evidently I (( Or, more likely, someone with the same name. )) am on some sort of government watch list.
The consequences of said listing seems to be limited to merely being required to get a boarding pass at the gate when flying, rather than being able to check in online. Naturally, this ends up with me being the last person on the flight. Somewhat annoying, but at least it doesn’t involve probulation or anything.
DHS has some cutesy-name appeals process (“Traveler Redress Inquiry Program” or “TRIP“) to explicitly whitelist a falsely-flagged individual. As annoyed as I am with the existence of the DHS, the TSA, and the process, I sent off the necessary paperwork and things should be cleared up in the next few months.
I wonder what could have caused this flagging to exist. I blog under a pseudonym, and in real life am an ordinary law-abiding guy. Of course, I was in the military for a few years, own firearms, use and strongly advocate the use of strong cryptography, have formal education in physics, and am applying to graduate programs in physics outside the US. I suppose that could be suspicious, but I doubt it’d result in something as minor as slight delays at checking in at the airport.