Hello,
most probably, this is caused by a fact that CAN communication is faster and there is a limited number of points configured for the Oscilloscope graph.
Go to oscilloscope properties and see the "Buffer" settings (I do not have a screenshot for old version 2.5). The number set there defines the maximum number of points the graph will be able to handle. You can increase this number.
Also, most probably, you have the Period set to 0ms (fastest possible). This means that the fast CAN is able acquire the maximum number of points in graph quicker than over a serial line. If you would set the period to 10ms or so, both CAN and serial would be sampling at the same speed and the graph would behave the same.
Regards,
Michal