Answer
That effect comes up if the trigger mode “Auto” is used. If no trigger condition is detected for 500 ms, the instrument triggers. That helps to see the waveform if no correct trigger condition is set. If the repetition rate is a little bit longer than 500 ms a kind of “interference” comes up, because there is no synchronization to the signal. The trigger will sometimes catch the pulse, sometimes not.
The only way to overcome that effect is to use the “normal” trigger mode. Then a trigger is done only when the condition (which is set by the user) is detected.