I believe I read a while back, that when a System Admin impersonates a Domain Admin they cannot use the chat.
If this is still true, which I cannot see the chat icon, so I believe this is by design, I believe it shouldn't' report them online to chat with.
It seems (Using the SmarterMail MAPI beta - But I think it would be a bug in the public release too), SmarterMail shows you online to chat with them you impersonate a Domain Admin, or maybe even a normal user, not sure on that.
I have tried, logging in as System Admin, going into a Domain, Manage, and when it opens up a new tab/window, it shows me online for the other people on that domain to chat with.
So I wanted to report that, see if it is a bug, and if so, make sure it is on the bug list!