The flame sensor and/or wiring would be my first guess. Make sure the position is good and all electrical connections are good.
Does your look like this? The model number seemed to point it was this new. Is yours a late 2003 or 2004 and newer?
I agree with Gene on the connectors. There is a small thermal cut off saftey that is natouris for not making the connection. It is inside a clear piece of tubing in series with T stat. If may be possible the heat or vibration of the gas burning is shifting it enough to break the circuit and that will shut down the burner and "not" throw a fault light.
Unplug, clean them up and put some dielectric grease on them. The Auto parts stores has it. Also clean up the PC board connector.
Yours is a newer model (rev 9 pc board) so you also have an electric element, does it work on electric? Also on the newer ones like yours, the T stat and the thermal cut off also work on electric.
I would say at this point it is not the flame sense system. If the flame sense did not work right then it should be throwing a fault light, at least along one line of thinking anyway. The fault light is only for the gas mode.
Since your heater fired right off, the control board is working enough to create the entire firing sequence, which is quite a bit of working. The igniter is also working and it "sounded" like you state it stopped sparking once it lit. Did it? If so then the flame sense is working as that is what shuts down the ingiter.
This seems to point to loosing the T stat and thermal cut off saftey circuit. If that path does not make, it shuts the whole thing down and will not throw a fault light.
If you go here and zoom all the way to the bottom, there is a 2004 Atwood service manual. Page 25 has the wiring diagram of the heater. Same one as the little diagram sticker on the heater under the control board.
Service Documents and Manuals
Hope this helps
John
