What are your values of PUMP START POINT and PUMP START RAMP parameters?
First make sure that the thermocouple extends about 1/8" to 3/16" into the exhaust cone. If it's not in far enough it won't see enough of a temp. increase and switch over later then it should.
PUMP START POINT - A good default value is AUTO+2. If it's less than that increase it. This sets the pump speed when it first turns on. A higher value will increase pump rpm, lower is slower. If you're getting a yellow flame when the pump first starts then lower the value.
PUMP START RAMP - A good default value is 6 . This parameter sets the pump rate of increase after it initially starts. 1 = slowest and 10 = fastest. If it takes too long to get to idle then increase the number. If you're getting yellow flames during Fuel Ramp then decrease it. The correct value depends on how strong your pump is and your fuel system restriction.
You may have to play with these parameters to suit your application. Use your HDT and pay attention to what the engine is doing during each phase of the start.
Joe