I have a very similiar problem. I just talked to am HVAC friend and he suggested that I call the gas company. Here is my problem:
Furnace turns on when there is a call for heat. Electric ignitor glows brightly, gas comes on. Ignites the gas, but it shuts off within a few seconds. Ignitor glows again, gas comes on, ignites for a few seconds and then shuts off. Does this about 3-4 times. It will do this mainly in the morning when the system is cold(er). We have an auto thermostat. However, if I force it to shut down and try to re-initiate the call for heat a few times, it will eventually light up.
After describing the problem to my friend, he suggested I call the gas company and have them check the regulator. Maybe the system is not getting the right amount of gas, is sensing that, and shutting itself off..
Don't know if this helps, but maybe it is a solution to your problem...