Twice in 3 days I have found the furnace blower running without the burners firing. I have changed filters and after shutting the system off allowing for reset (blower stops running) the burners light up. On both occasions the electronic pilot is glowing with pilot gas flaming.

Its hard to say with out knowing the make and model of your system. Sounds like you may have a dirty flame sensor. Scrape it clean with a knife or steel wool and see if that helps. Give us more info about the system if you can. Good luck.