Apologies for the lack of context.
I was using the MATLAB support package (aka ArduinoIO Pakage) from Legacy MATLAB and Simulink Support for Arduino - File Exchange - MATLAB Central.
The blue text is from the readme.txt file that I was following.
I resolved the issue. I changed the line (line 565 in the arduino.m file) from
errstr=arduino.checknum(pin,'pwm pin number',[3 5 6 9 10 11]);
to
errstr=arduino.checknum(pin,'pwm pin number',[3 4 5 6 7 8 9 10 11]);
which allows for the analogWrite function to be carried out on pins 3-11 instead of just the six pins listed originally.
You were right in that it doesn't change which pins can be PWM'd, but it does allow the MatLab script to be carried out without interruptions or errors.
Hope this helps anyone else if they are using the same package.