Never mind. I found out what the problem was. The parameters to the functions were slightly different. As such, the outputs were slightly different too.
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M-file s-function and c-file s-function outputs don't match. Why?
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I have a Simulink model that generates a square wave and passes it through two different s-functions and then plots the outputs. One s-function uses a m-file while the other s-function uses an equivlanet c code (turned into a mex file). Why are the outputs not the same? Is that normal?