Letters like S and O, U, C wil not be the same height as the T, A, N, I, L, etc.
The rounded tops and bottoms will be slightly beyond the 'straight' edges of squared-off letters.
This has nothing to do with what you're experiencing, but is just good info to keep in mind anyway.
In any case, the instructions within the above tutorial video show how to calibrate the 'Cutter Scale" (11:30 timestamp)