Ok, sounds like you will need to sort a couple of things out. Firstly the Trunk Attributes assigned to the Exchange Sip peer profile is not abosobing/inputting any digits when the one assigned to your public trunks is, probably best to assign an extension number to your Fax server and refer to that. Secondly SIP peers are seen as public trunks to the system, so when you try to use refer you are actually asking it to transfer externally, so check that the class of service assigned to the Exchange peer profile (and/or possibly the public trunks?) is allowed to transfer externally.