I will just add this to the thread.
I still have my SmartLinc (2412N) from before I got my ISY. Tonight, I plugged it back in, updated its firmware and linked only the thermostat - so I could compare the experience using the thermostat with MobiLinc via both the ISY and the SmartLinc.
In MobiLync with the SmartLinc, the Thermostat seems fully functional - it displays current fan mode (AUTO or ON) with the current state in BOLD. It displays current action of the system (COOLING, HEATING or nothing for idle) and the Temperature and Humidity seem to update nearly live - no refreshes needed.
Switching back to the ISY connection - still within MobiLinc - the fan status is not available, system status is not shown and I have to manually sync to update the temperature and humidity. The manual refresh does not get the status of the fan or system (Cooling / Heating etc) - that remains unknown.
The only difference seems to be the way the ISY talks to the thermostst.
If there are any traces I can take to help figure this out - I'm happy to do my best to help. I'm not convinced this is a thermostat issue myself - but it seems to be more of an ISY issue. See the album at http://imgur.com/a/358xN for screenshots of the two - note that the state of the HVAC was identical with the two - AC running, fan on.
Michael.