Stepper noise with mesa on new install

Hi All,
I have a system which I have repurposed to driver a Sherline Mill. Using their steppers but TB6600 drivers. 
I'm getting noise during steps. I thought it was the handle rattling but it occurs on all axis. I taped the handle to be sure.
If I run G0 X4, G0 X0 repeatedly, it doesn't appear to loose steps with one exception. The first move after Home runs
about 1 inch past where it should. After that, perfect. 

Sherline steppers
TB7600 drivers, 3200 steps / rev, 2 amp currently limit
Servo thread max jitter 152807
Base thread ma jitter 214347 (not great but I didn't have a problem before)

I tried editing the INI file to increase step pulse beyond the 10,000 that pncconf allows but it didn't make a difference. I did set it down to 4000 to see if I was editing the right place and the stepper no longer moved.

Any clues? 
   

I would check:
hm2_7i76e.0.stepgen.00.position-fb (for the X axis)

with halmeter or halshow to see if the
noise is from the drives or LinuxCNC

Power supply, what voltage for the drives?
One thing to check, disconnect one of the motors and measure the coil resistance, high inductance motors will not be good for bipolar stepper drives, and that reminds me, are the motors by any chance unipolar? And is the middle wire separate for the 2 pairs of coils?

Hey Peter. It's been a while.

Perhaps this is 2 problems.

Start LinuxCNC
Home all
Open halmeter and select hm2_7i76e.0.stepgen.00.position-fb
reads 0
G0 X4
reads 4.979041
G0 X0
reads 0.979041
G0 X4
reads 4.979041

The first time after a home, I get a move too far. After that, all is good.
Actual machine tracks these numbers, well as close as I can measure!

Hi Tommy,
Measured 12.14v. It's a 10 amp supply.
The Sherline steppers are indeed 6 wire. They didn't use the center tap and treated them as bipolar.

My experience before was a continual tone while the stepper was running at the same rate. This seem to have a crunching sound occasionally. I have not disconnected the motors but all axis produce this sound. Hmm, I didn't check to see if they produce the sound at the same time.

Thanks,
Steve

12V is to low, but still usable with low inductance motors.
Using 24V would be better, but first, the feedback does not look right, so wait for someone with more knowledge about that, then we can see if the voltage is enough to use the machine.