This craft has the throttle linket to Slider 1 in order to have 2 times precision. -100% is 0 thrust and 100% is 10 thrust, so the engine is working over it's max supposed value.
I was trying to make bigger than normal plumes and found that if you go over 100% the plume starts to dissapear for short periods of time, increasing the duration and probability as you increase the throttle.
The screenshot is taken with 10 times the max thrust and the fire looks like small bursts.
I'm takin into account the stretching of the plume particles, the bigger the effect the more it stretches. But the lack of fire is not related directly to particle stretching since it doesn't happen always.
I know this is a not intended behaviour of the engines but with the introduction of custom engines and fuels this may cause some problems.