Due to mechanical inertias of the generator and voltage regulation that is less than the regulation of the utility grid, I suspect that voltage sags from the generator are causing the flame sensors to fail to see the flame.
Sag Correction for Small Equipment Without Using UPS Systems
"The most common power quality problem encountered is that of voltage sag. All equipment is susceptible to dropping off line if the incoming voltage is low enough for a long enough period of time.
"Publications found in the trade journals give the following generalized typical equipment shut-down characteristics...
"* Boilers with flame sensors may indicate a loss of flame with voltage sags, thus causing needless shutdowns." http://www.powerqualityanddrives.com/sag_correction_without_ups/