I believe the no-fly and watch lists vary depending on the airline. I flew with two friends on American Airlines from DCA to MIA back in October, and one of them was flagged because his name (a common Arabic one) matched four terrorists' names. It took a while at the ticket counter to clear him, and his boarding pass printed out with SSSS. However, this same friend flew US Airways out of LGA just a few weeks before and had no troubles. This may be what happened to you; it sounds like CO may have updated its lists recently.

Contact your local FBI field office; they might be able to help. Good luck!