I have the same problem. I've always assumed it has something to do with my macros though. I don't know if you have it set up this way as well, but I have Fast Blade macro'd with Bloodbath and Fight or Flight, so when I tap my R2+circle it does one of those three things. But when Bloodbath and ForF is on cooldown, I think the game gets weird and it isn't smooth in casting Fast Blade. Does that make any sense?

The new controller thing also could make sense. I've had this controller as long as I've had the console, and I got it back in 2008 if I remember right. It's never failed me though!