Something else to consider is the load impedance that the pedal/guitar is 'seeing'. Most amps are typically 1M ohm input impedance, so is your Cro which is replacing the amp also providing a 1M ohm load to the pedal/guitar? I'm suspecting your Cro's impedance may be a little higher leading to the 'discrepancy' that I think I'm seeing in your bypassed screen shots...
1M per volt is not a 1M ohm load.. and a x10 probe is definitely not 1M ohm i/p Z.