Usually the rollout switch will trip from having the flames rollout for some reason or the other. Where is the furnace lacated in the house? If your returns were restricted by the 3m filter and drawing from the holes in them this could have caused your furnace room to go into a negitive pressure and draw the flames out. Its hard to say from here without more information. Also the lack of a chimney cap and windy conditions could have caused the same thing.
I would highly recommend getting rid of the 3m filters. They have killed more furnaces around here than I can remember. They are much to restrictive (even new) and most duct systems are not designed for that.
Any of the service techs that you had out should not have only told you that your furnace was bad but also explained what was bad. The salesmenn wouldn't have been able to do this.
Hopefully the last guy out (more than likely on a free estimate) will get compensated from you if his repairs work.