pwm schematic help required please?

[Voicecoil]

The direction is switched via relays on the other board (I assume as they click when direction is programmed), the voltage from the breakout board when I mdi input s240 m4 is 0.5v, then at s500 measures 1.0v, at s1000 2.0v etc etc.

It would be instructive to measure on that same point with your meter set to AC rather than DC whilst inputting s240, s500, s1000 etc. and see what you get: if there's a decent (a volt or two) AC level there at s1000 then it's a PWM output, if not then as Doddy says it will have been converted into DC. A DC meter will average out a PWM signal and give a reading corresponding to the duty cycle:

The AC level will be zero at 0% and 100% duty cycle, but doesn't vary so much in the middle range.