Hi, We have read most of the posts here, for the snuffing pilot light, and it is wonderful all the helpful people out there. We have an old, propane gas furnace called a J-Line by Moffat. To give you a little history, it has about 30 years of history. It was used part time to heat our house for the last 20 years, we use wood as well and full time for the folks that lived here before. It sat for about 3 years when we did not use it at all, those 3 winters, we stayed home a lot.
Then we had a professional come in and fix it, as it would not run. He replaced the inline fuel shut off, he cleaned the burners, and replaced the thermal coupler. It ran, for about 3 weeks and then it went into the intermittent stage, as it has since. It was making a very loud noise when it would restart too.
But since we have done the latest cleaning on it and changed the position of the stand for the pilot light, as we noted it was not where it was before the other guy fixed it. As well we have replaced the thermal coupler, again just recently, cleaned the pilot light (blew it out with compressed air), and cleaned the burners too. It seemed like it was fixed the other day and we both had to go away, and it was working fine, except sometime while we were gone during the day, it quit again. The pilot light was out again.
We have it going right now, there is no rhyme or reason to it, it has cycled 5 times, and my husband is watching it in hopes that he can find out if there is a sequence to it's quitting. It just made a drain sucking sound, which my husband says he has heard before occasionally, he says it is the burners, and now it is okay again. This is so frustrating I sure hope you can help.
I have long thought that it has something to do with the baffles in the top of the furnace, which have become disloddged over the years and have been randomly tucked back up there. I think it's an air problem or a thermostat problem. But then I don't know anything about these things.

If the pilot flame is not hitting the thermalcouple at all times the gas valve will shut off. Low gas pressure,crack in the heat exchanger or face plate, will make it do this. When the main burners come on does he pilot light get smaller an move away from the thermalcouple, or when the blower kicks on does it blow the pilot flame around and away from the thermalcouple?

And yes the baffles could cause your problem due to a draft coming down the chimney and blowing the pilot out

If the heat baffles was restricting the exhaust the main burners would be rolling out of the heat exchanger. The heat baffles or plates that set at the top of or out going side of the heat exchanger are to restrict the heat so the heat exchanger can heat up.