I had an experience very much like Rod describes, I think.
I believe the creases were in the cloth right from the factory.
The cloth came on a roll, and the creases were extremely regular - parallel,
evenly spaced and of very consistent width. More of an indentation than a crease, really, about half an inch wide.

I couldn't get the glass to stay flat on the hull, no matter what I did.
I got long thin raised areas that would come back every time I pushed them
down. I ended up just letting those areas float, so they aren't bubbles, but
slightly raised, solid areas. I chose to leave them rather than try to sand
them off.

I used the exact same glass with the exact same creases on the deck, using the
exact same technique, except for one thing, and the deck came out perfectly.

The only difference was I seal coated the hull, but did not seal the deck.
That made all the difference for me. Different surface tension, maybe?
I don't know.

In any case, I don't do seal coats any more, and have had no problems since.