Bob is correct about the proxyAddress attribute requiring a sip:email@example.com to make presence in Office/SharePoint work; however, I don't believe it is relevent to your problem.
Right now our email address is a different domain then the IM Address. Is this OK? Should they be the same as the email address?
Yes unless you want to do inter-domain federation to the outside world. If you plan on doing that at some point in the future you will: a) need to own the domain so it has to be legit not something like a .local TLD; and, b) users would have to advertise the separate URI to others who want chat with them. Ideally, they can just reuse their email address for this. If you want to do federation the servers and the presence domain should be your public DNS namespace.
I have someone else testing and for them certain peoples contacts are showing both the email and IM address being the same. The IM address is not using the Windows @domain. Its using the email for both.
Does that user have an Outlook contact for these people? In the current releases, Jabber does not support "pizza guy contact" so it can't get this from the CUPS/IM&P server; it must be getting this locally. My guess is there is a personal Outlook contact for it.
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