I recently took up all of the plywood floor from my storage building (12'X16') in order to place a moisture barrier on the ground beneath. I then placed new pressure treated plywood (3/4") over the floor joists (2"X6" spaced 16" apart). The floor is supported underneath by a skid which runs down the middle separating the 16' width into approx 9' and 7' sections. Now that the the new floor is down, whenever I walk or make any sudden movements on the floor, I notice it shakes which I'm sure is because I cut the old plywood out around the perimeter of the floor and is not as stable. Is there a way I can stabilize the floor better?

Several questions to clarify things
Where is the floor the shakiest?
In the middle? Around the edge?
What sort of packing is beneath the joists, and is there an air gap ?
And where the skid is fitted how is it secured? By clamps/bolts?
My first thoughts are the skid is unevenly tensioned . And one half (or quarter?) of the floor is not under the correct stress.
Hence you'll see nails getting pushed up eventually
The other 2 possibilities are there is an air bubble trapped where you packed the moisture barrier(if its the PVC sheeting?) and created a high (tight) spot or spots with the surounding woodwork feeling "loose"
Cure with out ripping up the floor is easy work out where the high spot is and drill a small hole to allow air flow under the floor(drill away from the joist)
And once you have started filling your shed again, the weight load will push the highspot down and the bounce will disappear when the floor settles
No ventilation to the moisture barrier is going to produce warping of the floor in the long term ... The material may "sweat" in Humid weather and with nowhere to go wetspots will almost certainly happen (Works against you!) Drilling the holes helps trapped heat escape
Better still consider making a small vent slot or 2 outside with access to the underneath of the floor I'm sure this will help matters a lot