Ok, first off I apologize if I don't explain myself and my question well enough but here goes. We installed a Honeywell RTH111B1016 (replacing an old dial type unit)we hooked the wires up as the were installed on the old dial unit. At first when we would turn the heat on both the outside unit and the gas furnace would both come on. After removing the jumper from the are and RC and leaving the red wire connected to the are we have heat but the Ruud unit outside for the A/C does not come on at all. That is the first issue the second the heats runs but it sounds like it cycles, meaning it sounds like something is running but heat does not blow out all the time. Usually it does this 5 or 6 times. Another thing I have noticed is that sometimes in the morning when I get up, usually the thermostat is set for 65, the Thermostat is showing the temp at lets say 63 and Heat on is displayed but there is nothing running at all and to get the heat to come back on I have to turn the thermostat to off and let it sit or swap over to cool and then back to heat to get it to come back on. I think we have all the jumpers and setting set correctly but I am still unsure since I have not heating and air exp. If it helps the gas furnace was replaced about 7 or 8 years back and I am almost 100% sure is less then 90% efficient.

You did a fine job of explaining,, but without being there to look over your problem ,it is hard to give you advice
It sounds like you still have wires hooked up wrong, but can`t see from here
Get out the install manuel and one at a time see for sure if wires are where they belong


,, Good luck,

Finally figured out what the issue was one of the jumpers on the Thermostat was incorrectly set but even after correcting I am still having the issue with the Heat On Indicator showing on the thermostat but nothing is running as previously mentioned.