In that case, check with a voltmeter the voltage your BOB is giving out to the VFD, both when jogging and when not.
In should not change.
Are the pin numbers on the BOB all pre - allocated - e.g. axis 1, axis 2 etc etc - and you have to set Ports and Pins to suit ??.
I can only think that you have the same pin allocated to the Spindle "step" and to an axis "step" Without jogging the PWM (Pulse Wave Modulated) is OK. If you can imagine a square wave of a fixed time interval, - then on 0, all the wave is at 0, - at 50%, half the wave is at 5v and half at 0v, - at 100% the wave is at 5v all the time.
Step signals to axis motors are pulses, square wave with a fixed time span (depending on your time settings on Motor Tuning) - the frequency of the pulses depends on the speed of the jog.
If the two are combined, then the axis stepper pulse will turn off the PWM pulse for some of it's time,(the 0v pull down pulse being stronger than the +5v) and so the converter on the BOB will translate this as a lower voltage.
A very detailed idea of what I think is wrong - but short of something actually being faulty, I can't see what else it can be.