Any way you can bypass the BOB and connect direct to the port or a second port? From what you say its working as far as the BOB inputs.
Yes AC servos are the mutts nuts, auto tuning is good but I find I can still get things sweeter with a further manual tune. Not sure of your drives software but the scope feature in mine makes tuning a lot easier, can monitor up to 4 things at a time although I usually only monitor the three. When Velocity tuning its commanded velocity, feedback velocity and error. For Positional tuning its Position command, feedback and error.
Was messing around with the lathe the last day testing out my netbook with the USB to Serial adapter, monitored both axis and homed, count zeroed in software and commanded a positional G0 move via Mach, most I saw out of position, with probably 50 moves of varying amounts on each axis, was -1 count, not bad when there are 8000 per 5mm
Hood