oscilloscope – Digilent AD3 Voltage Waveform Jitter

This is not related to the trigger level, but to the trigger holdoff. Holdoff is the time after a trigger event happens that the trigger is disabled, and when triggering on burst waveforms like this, setting holdoff appropriately is essential.

I recommend setting your trigger holdoff to some value longer than the length of the burst, but shorter than the time between pulses; that should get rid of this jitter. If the holdoff is less than the length of a burst, then the holdoff can expire in the middle of a burst and trigger again on a later edge within the same pulse, causing the effect you see. This will also happen if the holdoff is about the same as the burst period, such that the holdoff period expires in the middle of the next burst.

As for how to set the holdoff, you’ll have to look through the trigger settings yourself, or read the manual; I’m not familiar with either of the oscilloscopes you mention using. All digital scopes should have a trigger holdoff function, though.