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Originally Posted by Mike
I just set the coupling to "DC50Ω" and it's still doing the same thing
EDIT: Same thing, but Output A isn't showing anything.
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The wave form output you gave, (and by the way, that goes a long way in helping us understand what you are dealing with, good work!

) displays a classic waveform display of a square wave read through an AC coupled channel. I am not familiar with that particular scope, so when you say you set it to "DC50Ω", I am not completely sure what that means for your scope. I can only assume that it is not correctly "DC" coupling probes 1 and 2 which, according to the picture, are connected to channels 2 and 3 respectively. The part I don't follow is the "50Ω" after the "DC". That is not a setting that I am familiar with for any scope. Also, as Manoel stated, for correct calibration purposes, make sure the probes are set to the same attenuation value that the scope is looking for. Some scopes do this automatically, some do not, so just double check it.
If possible, can you put up another picture of what your screen looks like with the new "DC50Ω" setting?