Hi Elliot, I'm currently dealing with similar issues in Simulink. What I've noticed is that matlab does not directly support reading out PWM frequencies. You said it worked from the arduino IDE, but I'm not sure what you exactly read out there. What worked for me was to configure the pin as a digital input and use readDigitialPin() to get out the signal. Then you can use a simple edge detector algorithm to get the time in between pulses and from there get the PWM frequency. Just make sure that the sample frequency is at least double the PWM frequency that you try to capture.
You can also try to do this in Simulink and see if you get a different result.
If this still doesn't work, you can also check your hardware. Make sure to use a common ground and a pull-up resistor, etc.
