A floating floor should not be attached anywhere. And, your contractor is right in saying that a peninsula/island in the middle of a large area...AND subject to radiant heat can be problematical, especially if the island or peninsula rests on the flooring.

Floating cork is specified over radiant heat all the time.

There has to be expansion space and the floor cannot be glued down anywhere or the problems you experience will happen. It wasn't the cork, it was the uneducated installation.

So he wants you to buy a floor twice, because he screwed up, and now he is going to have his clueless laborers install another floor for you??? I see even more corners getting cut during the second time around.

I'll join the chorus: I think your builder is going the wrong way: the problem isn't that the floor wasn't glued down enough. Quite the contrary, it was held down too much.

In addition to the reccomendations above, check your heating system: how hot is the water going out to the floor, is there a system in place to turn off the pumps if the floor gets too warm?

I'm still learing the ropes with mine, it's far more complex than normal thermostat, on/off system.

In your specific situation you really need some expert flooring specialist to come in and make a physical inspection. It is very difficult for anyone to give you the best answers on a forum. Plus, if it would go into litigation a written examination by a flooring specialists would help you. Be sure to get a copy of the manufacturer's written warranty and written installation procedures.

Thank you for the feedback. I am fully aware that my GC has voided the warranty on the flooring. Not only did his laborers glue the floor down in some areas, but they also did not use a vapor barrier, (couldn't if the floor was glued down right?).
There is no place in the house where any large amount of weight rests on the flooring. The cabs were all installed first and flooring installed up to the edges. Same with the fireplace peninsula and the island. The flooring was on the sight for weeks before the install, and stored for 3-4 months less than a mile from the house.

We are waiting till it gets a bit colder to do the checks on the heat levels of the flooring. The problems have manifested over the colder months. The plan is to test for heat, make decisions regarding replacement of the flooring and then reinstall the flooring in the spring when we will be gone for two weeks.

I am personally confident that the problems are due solely to the glue down of the floor. Every place that we have a crack or gap is at a transition of some kind where glue was used. Additionally the upstairs which was not glued anywhere, because a professional flooring crew did the job, is perfect. We do have some contraction around the walls, and because we have very thin baseboard we can see some of the gaps. These gaps are right near the walls and are mostly hidden. I feel that this type of gap is expected and is acceptable to me. I don't think cracks in the middle of kitchen floor and elsewhere are normal or expected. My husband an I installed the floating floor in our last home over radiant heat, it was Kahrs click and lock wood flooring. We had none of these problems and the systems are very similar.

This is not the only problem we have had with our contractor. We are still holding back on final payment, although by the time we are issued credits the total amount isn't near enough to pay for the floor.

Boxiebabe: Regarding credit card payment: even if we had paid with a credit card we are well beyond the 60 days a credit card company will allow you to dispute a charge. Did you manage to dispute the charge after 60 days?

I was really curious to see if anyone thought that gluing down ALL of the flooring sounded like a solution. I do think that even if the floor was properly installed having the two peninsulas and the large connected square footage could be a problem. Perhaps the total glue down is some kind of solution.
I realize that the GC is trying to cover himself by suggesting that we chose a poor material. He has stated that no one locally will work with cork and that the industry trend is away from this material because it is so problematic. Unfortunately we live in a pretty small resort community finding a "flooring expert" is not as easy as it sounds. The nearest city is 280 miles away.

You can only glue down a product that is designed to be glued down.

Sounds to me that the install was faulty. But you do need an independent flooring inspector to determine what was done and what went wrong.