Hey Bob,
I'm in the process of writing a Transceiver Toolkit tutorial.
I was just at the point of using the TTK GUI under Quartus 15.0 and its broken, eg., you cannot control the transmitter at all (the start button remains greyed out), all sorts of other weird stuff. Using Tcl I can access the transceiver registers directly, turn on the loopback, pattern generator and checker, and confirm that the loopback link works fine. Some of these changes show up in the TTK GUI, while others do not.
I've just tried Quartus 14.1 and it has similar issues.
I'm about to go back to 13.0sp1 (since I have it installed), and will then try 13.1.
Let me know if you found a version of Quartus where things worked ...
Cheers,
Dave