Is this brand new or did you just notice it?
Can I clarify a few things?
-she's not shaking when she's asleep
-she's waking upt at normal times
-shaking is only when she's waking up?
Could it be she's stretching as she's waking up. I think my dogs probably do that a little bit, I woudln't have really called it shaking but they do move around a little before they actually wake up and if they are in their crates perhaps they might do this longer since they don't have as much room to stretch?. If you are really concerned about it, I'd definitely ask your vet just to be sure.
(a.k.a. Lucky's & Sparky's mom!)