I wonder how often, after reviewing your details, DHS lets the airlines know that you're clear?

My case - couldn't check in online with USAirways, they tell me it's because of DHS action and I should file a report (I have a common name). Duly file the report and, after a few weeks, I get my letter from DHS saying that I'm in the clear. However, since the letter arrived I've still been unable to check in online (going to the US Airways desk at ORD is a not a big hassle - there's never any line - but nevertheless...). I wonder if it only applies to future bookings and not ones already in the system?

Steve