Was the burner doing the same thing before you replaced the old control? if the pilot flame signal is strong and the failure happens every now and then chances are the ignition transformer is going bad.
Yes. I replaced the control to determine what stage the burner was failing... That's when I found it was ptfi.
I stayed at the job late one night this week ( i forget what day, im working now from 6 this morning!) watching this thing run. Although it did not fail the incoming gas pressure to the building dropped. I couldn't get enough pressure so utility comp came out and made adjustment to the regulator.
I'm still not out of the woods yet though. I have to adjust the burner a little and check a valve for a possible restriction. So we're getting close to the answer. I'll fill you in when I know for sure. Thanks