Did you purchase the Gatorskins that were folded up? I have the Gatorskins that came in a large box not folded. Love the tires.... after all I live in Florida and gators are also house pets......

From what you are saying sounds a little like there is some delimitation going on inside the tire carcass. I don't know about bicycle tires, but other tires are laid up in various diagonal layers with the carcass inside-out then they go through a heat process. Up until recently this lay up was done by hand. In the 90's I visited the Bridgestone and Dunlop plants in Japan... what a hot and smelly labor intensive job. These produced automotive tires.

Couple of things that can cause carcass separation is very high speeds or low pressure causing excessive heat buildup. I really can't see these in a bicycle tire. It may be reasonable that the tire was way over inflated at one time.

Also, riding along smoother painted stripes in the road and riding on the rough road surface will produce different sounds due to the coefficient of friction differential at the tire/road contact.

If you have the old rear tire I'd cross section it at one of the soft bubble spots and see if it is delaminated. And I'd contact Continental and ask their tech folks. Importantly, I'd be highly suspect of the tire.