I have an Airco 2-Stage furnace that was working fine with a Lux thermostat. I changed the thermostat to a Honeywell WiFi thermostat so I could control it remotely. After installing the thermostat based on the install instructions it weemed to work fine until the 2nd stage kicks in on the furnace. When the 2nd stage kicks in the furnace cuts out or powers down. The furnace then comes back on by it self but it starts again at stage one and then will cut out again when/if it has to go to the 2nd stage. I used a 'G' wire bypass on the thermostat install because the thermostat requires a 'C' wire for power and there wasn't one. (not sure if that has anything to do with it. I called Honeywell and they said it is wired correctly according to the Honeywell thermostat specs.

Any ideas?
Thanks.