I'm trying to install a wireless thermostat but i ran into issue putting in an external thermostat. I have a 2 Stage Cool / 1 Stage heat system.
I have the Red 24V from Air Handler connected to R. I have a external 24 Volt Transformer Hooked up to Rc, and C. I get 27 volts between Rc, and C. However when i tell thermostat to turn on fan nothing happens. If i remove external transformer and jump Rc, and R using AHU transformer everything works fine.
What could be causing this?

Cwire, but in my opinion it's not the best way to go. The correct thing to do, is to run a new cable with an additional wire. – Tester101 Sep 05 '14 at 00:17