struggling to tune Z axis

Hi there
been retrofitting a plasma table using DYN4 servo drives and motors, through a CSMIO IP-A motion controller and Mach 3
X and Y axis proved very easy, but Y axis is putting up a fight,

I have the Line number set in the dmmdrv software for setting up the drives, as 4000 which should mean 16000 pulses per motor revolution, but i noticed that in the csmio diagnostic window in mach3 that the Internal Position Counter was showing 32000 counts per motor revolution.
Also while one motor revolution physically moves the Z axis 5mm, mach3 reads it as 10mm.

At these settings it seems to auto tune ok and behave itself, until you jog with the page up/down on the keyboard, it then goes into quite high frequency, but fairly small oscillations,

If i change the steps per number in motor settings to x2 what it should be, mach3 reads the correct 5mm per motor revolution when i turn it by hand, however when auto tuning it goes mental and oscillates wildly

Any ideas to try?

cheers!