My guess is they're just mis-informed or lazy Captains who don't often use a jumpseat or think of how their professional courtesy affects others around them. I've had it happen to me on a couple occasions - maybe once or twice on US Air (I previously worked at a wholly-owned) and once on a United 747 from HKG. I just shrugged them off as anomalies, based on my many other (very good) jumpseat experiences.
I don't think there have been any policy changes at US Airways. Most captains, I would expect (regardless of the airline), would always prefer you to poke your head up and ask permission to ride. After all, it is the Captain's prerogative to grant access to the jumpseat, whether it's as a cabin occupant or sitting in the actual seat. Captains who don't expect jumpseaters to ask permission are undermining their own Captain's authority - something I think many would agree has been eroded enough already.
As for the flight attendants acting like an agent of the SS and stopping pilots in uniform at the door.... I am usually annoyed by it. I don't know what their manual says, but at least treat me with professionalism. It's something that's annoyed me for years now. But I was able to deal with that more easily than a pilot who brushed me off.
Summary - I always ask the Captain, because I know that's what I would want if I were him or her. And if the FA wants to act like a storm trooper, oh well, go ahead if it makes you feel better.
If you ever run into any problems, I've found jumpseat committee chairmen to be very receptive to both questions and issues. Call yours, if you have one, and deal with it that way if you have problems or questions.