I'm assuming you have this info on hand (see link), older Engineered air systems had very poor turndown capability and to compensate for that they cycled the snot out of the burner. Problem being if you have inconsistent ignition you get lockout. Their control system is very basic (maybe a little too basic), any of the units I have had problems with were usually due to intermittent pilot ignition cycles and once that was solved all my problems went away. Hopefully someone else has some more direction for you.
http://engair.com/manuals/Q7LxO1a22.pdf