Dwaynes use a motion picture processor for their Kodachrome line, maybe they're running a similar thing for E6. How it works with the kodachrome is that all the rolls are spliced together and run through the machine as a continous roll. If you were to get some a jam in a machine like that with a polyester based film, you'd be looking at some problems.
I've used plenty of polyester based films in my 35mm cameras (with motor drives) and have never had a problem. I've never heard one story on APUG of a camera fault chalked up to a polyester based film either. And there's enough of us here...Remember, Kodak HIE and EIR were on a polyester base too. It's not just those nasty folks from Rollei.
Take it to another lab and be up front about the fact it's polyester based and ask if they would have any problems with that. Apparently Dwaynes do, and that's good to know. My local lab doesnt.