Yes, with the information provided we were able to get the phones to authenticate EAP-MD5. Since we are using NPS 2008 we had to edit the registry to turn EAP-MD5 back on (link here for reference
http://support.microsoft.com/kb/922574 )
Unfortunately we still aren't able to get the computers to authenticate when plugged in through the phone. If we put an unmanaged switch on the Enterasys port and plug the phone and computer into that, they both authenticate fine so we still believe this to be an issue with the phone not passing the request up to the switch. We are working with our ShoreTel partner to find a solution. If / when I get that I will post it for the benefit of others.
I have also reached out to Scott in a GTAC case with some wireshark captures to see if he can come up with anything that might help come to a resolution.
Thanks to everyone who replied,
Matt