Same story here. I was often delayed by 45 minutes or more. Basically, I as a native-born American citizen with no criminal record (and ironically, worked for the DoD at one time), could not board a plane without the express permission of the government such that I was delayed while waiting for that permission. Everyone I was traveling with was allowed to go on, I was stuck behind. It was a real source of difficulty for me for a few years. At some point it went out of sight, though I still received special treatment at the border for a while.

Consequently, I have a pretty negative view of the "no-fly" lists. Anyone sufficiently dangerous to put on the list is sufficiently dangerous to be arrested. Anything short of that is an obvious lack of due process.