While you have set them to the same settings, they are probably at least running different frequencies.
I would suspect that the remote on the right has a very low frequency as only the left LED is lit in the pic. Low frequencies using the square wave with no offset would result in a slow oscillation between LEDs.
I would then suspect that the middle remote had a fast enough frequency that both LEDs appear lit at once.
As for the right remote, the frequency may be very high and thus the LED does not get lit long enough to produce the same amount of light before it is switched back off.
If the frequency is not accounting for this (hard to say with the information provided), then simply take the remote on the left and place on the middle generator and compare.
The LEDs are lit by siphoning energy flowing to the coils. I have some remotes that will not light at the same threshold as other remotes using exactly the same settings/amplitude/frequency.
I suspect that there is a slight variation in tolerance between remotes as to what amplitude the LEDs will energize well.
Since you were using 5v, you are close to the minimum amplitude limit for the LEDs to light and so maybe that one remote just needs a bit more power to light as well, more of the power being directed to the coils.
One thing you can do is try using a 20v square wave and compare when there is plenty of juice.
Either way, this would not affect the efficacy of the coils.
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