When the heater lights is there a hard whooshing sound? If so, then you might be experiencing a "concussion" light.....this means that the gas puddles before igniting and "explodes" when it hits the pilot flame. This concusssion will extinguish the pilot and the pilot generator will start to lose voltage until it drops below the minimum required for gas valve operation.
Sounds like when burner kicks in it is diverting gas away from pilot. you have either too low pilot heighth or more likely an obstruction in pilot assembly
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