That kind of voltage response is what I would expect. I presume that is Mach3 with a parallel port connected to the G540, right?
It is very interesting that with the PMDX-411 you always get 6.63V. I would have expected something close to 0V if the PWM from the 411 weren't working at all. 6.63V is mighty close to 1/2 scale, and is what I would expect if, say, the charge pump signal were actually being output on the PWM pin (even though the charge pump frequency is MUCH higher than the 50Hz recommended PWM frequency).
Do you have the "charge pump" switch on the G540 set to "On" or "Off"?
With Mach4 "disabled", what voltage do you see between G540 terminals 7 and 6?
Please post your revised profile (create a new profile package). I don't have a PMDX-411, but I can try this on my 422 and see what it does with the PWM.