OK - your reference to PWM threw me a little as you have connected up according to rawcnc link.

This is using 0-10v analogue control on the right hand side of the BoB in the link. This may be derived on the BoB from Mach3 PWM output which is presented on the PWM terminal of the BoB from the pin 1 output of Mach3. The on/off spindle relay is used in your case. My spindle speed control is via a SuperPID device http://www.vhipe.com/product-private/index.htm as I have a Kress router on my small machine.

The strange sound you refer to in the motors could be a result of an intermittent disconnected winding as only one coil is being energised and with the change of direction of flux it would just buzz at the speed of the driver pulses.