We too love our Seneca 35GS.
Here is the Atwood installation manual with some initial test instructions, wiring diagrams, and some troubleshooting for your furnace;
Excalibur 8900 III Series Heating System - Atwood Mobile
Atwood also lists their contact phone numbers on the first page of the manual. If all else fails it might be worth giving them a call.
There's also lots of information from other owners including troubleshooting steps with a Google search for the model 8940-IIIDCLP.
Let us know what you find is the problem.
We have had the same furnace in the last 3 motorhomes over many years but never a problem. Of course we live in Arizona so we don't use it that much either.