It happens on PC too - I have both. I actually DPS on my BLM on PC and I prefer tanking on PS3. I do sometimes run into having to hit Fast Blade 3-4 times and freaking out because I'm not sure if I am lagging or what, but I find movement and flexibility greater on PS3, everything is at your finger tips as opposed to a PC with a traditional M+KB where your buttons are all spread out, and you might have to take your hands off your movement keys to silence/stun/etc.

You can tell if its your controller or not by paying attention to the skill icon when you are trying to activate it. Every time you attempt an activation it will light up white for a split second to show that attempt - if its lighting up, its not your controller.