> I have not had a problem with this. In my jigsaw I use a blade that cuts
> on the up-stroke so the base of the saw holds down the glass.

There are blades availiable for jigsaws that cuts on the down-stroke. Using one of theese, the blade will always push the glass layer against the wood while cutting. You'll also get a cleaner cut on the surface.

Another way to go is to cut from the under-side of the deck. This could be difficult depending on how much the deck is curved and of course if its already mounted or not, but with a normal blade in the jigsaw you'll still get the effect of pulling the glass against the wood while cutting. If you have a pendular jigsaw ( i.e. it pulls the blade back a little on the down-stroke) it-ll be even safer. I've used both methods while cutting fiber plates with veneer surface. Works fine.

Totto