Now the key question which of the timing is off, the scope or de Arduino. I guess the Arduino. Can you make a .psdata file of something with a exactly known frequency at the highest sampling rate possible with your scope. Be sure you set the number of samples to the max (100MS) as in image below 202...
I think there is a misunderstanding. The math data is always calculated by the windows PC, but there are 2 situations. 1. live view (the math channel data is calculated and shown from the downsampled data) this is because during live view (in all situations ?) there is only downsampled data send to ...
Some hints on setting up the right way
1st set your scope to +/- 10V instead of 5 because you have overvoltage and the decoder can have problemens with overvoltages.
2nd your signal seems te be inverted so you need to setup as shown below.