So almost a year on, we thought we'd solved the issue,but it was still grinding.
Not voltage, still jumper issues
Cheap copies of A4988 pololu drivers (still marked the same) only support 1/8 microstep not 1/16. MS3 on ramps boards literally does nothing. So if you think you've set 1/16, you've actually enabled full stepping. 1/32 (which we had working, sort of) was because it was supporting 1/2 rate stepping, as MS1 and MS3 where MS3 does not work = half step.
D'oh.
Finally sorted. Everything works great. Been a long trek but I'm finally happy.