It's all about input.
To pull of certain moves you need to do certain patterns within X frames from the first input. Things like this were a lot stricter in Street Fighter one where everything had to be frame perfect.
I don't know what USB controller you have, but, in games like Street Fighter, it's down to how well you can use that input. For instance, gimme an Xbox 360 controller and I'll pull of 720 spin moves pretty easily. Gimme a keyboard and watch me struggle to pull off single-rotation moves.
It'll take some adjusting and getting used to, but eventually, as you grow more comfortable with the USB controller, you'll pull off moves more consistently. Just give it more practice :)