Dunno how old your amp is or how many hours are on it, but it could be the tube.
I had some issues with mine and replaced the tube.
Still had the same thing, would make some noise sorta like you described.
Contacted GB, and they said send it back. Problem was, it's my only amp right and I had a TON of gigs. And the noise wasn't getting to FOH.
On a whim I replaced the tube a SECOND time.
Problem solved.
Just for giggles I'd give that a shot.
The Shuttle 3.0s have no tubes... they are FET preamps. Good info though.