Thats weird. I would definitely replace it and also call the guy and see if Flexwatt has a customer support line and call them. I cant give much help as i have never used the new flame retardant stuff. i just use the original flexwatt and have never seen any weird scorch marks like that. Are the marks also on the bottom of the tubs?

I cant imagine it would be getting too hot as i assume you have the probes sitting directly on the flexwatt so no matter what you put on top of them, they will only get as hot as you set it because the probes are sitting directly on the flexwatt.