Can you go into test mode by leaving your jumpers on teminals 1 and 2 and pulling them off when the unit goes into its heating stage? How long will it run then? You can single out a control problem that way.
Make sure all of your safeties are made and auxillaries are staying made. You may need to take an hour or so to check them but you have to make sure.
Check the board('s) look for any shorts or water damage.
If it is a "power" burner make sure your screen is clean and your tubes do not have any cracks at the bottoms (heat exchangers).
Definitly check your pos-neg pressure tubes to make sure they are not filthy.
Had a unit do the same thing and found an Auxillary faulty, it was located behind the main 3 pole 480 volt main breaker on the unit.