Found the 'problem', see image: (It's in you scope settings...)
Error: You should not be triggering on both channels 1 and 2. Only trigger on channel 1 exclusively, otherwise, channel 2 will randomly or find the next trigger event and re-align to a non-parallel position based on its waveform completely screwing up the whole purpose of the differential measurement. (IE, the scope is waiting for a trigger on channel 1, then it waits again for the next trigger on channel 2. You do not want that. Channel 1 and 2 need to be aligned in parallel, so, you should only be triggering on 1 channel.)
This is assuming using 2 separate triggers on 2 channels simultaneously does the same thing as it would do on my Tektronix scope. With this setup, my scope would generate the exact same error and doing this when attempting the same A-B 'math' differential common-mode measurement, the 2 channels are no longer aligned giving me a flawed result. The math is being done on the sample data in the window with the relative alignment position you see, not like an old cathode ray tube analog scope where the input A-B function is done at the analog stage in the probe input amplifiers where such an alignment error could not be made.
Once again, if set correctly, my test#2 above, with Channel 1&2 on the same VCC should generate an identical signal on each trace while the 'math' channel should show dead flat 0.
The 50msps should also be able to be increased by using a longer record length as the Owon scope in use can do 1ghz, with a 10 million sample record. Increasing this setting would generate a far greater refined scope shot and more accurate measurements even if you keep the horizontal zoom level at the current 5us/div. (Assuming the Owon has enough ram, otherwise, the only way is to zoom in the time-base.)