Driving me insane

[Bush Flyer]

Yes it's always the same axis that goes wrong X and A axis slaved. One stepper motor stops and the other keeps on going. I did a small line picture the other day and it started fine then half way through the cut it moved the rear part of the picture 12mm away from the front part. It will run fine and I even rerun a g-code today 11 times over the same picture and it will follow the same line spot on, then for no reason on the 12th time it will go and cut a line short and mess it up.
The first time I really noticed it was when I first fitted a spindle and VFD in place of the router, Also when I first switched on the machine and seen it move for the first time, it did crash in to the limit switch for no reason I was jogging the x axis then it didn't stop but it's been OK till the spindle was fitted, Having said that I have seen it go funny with out the spindle running, on just a test run no end mill fitted.
If I lower the acceleration down to 200 will this cause a problem if I try it at this setting for a few days.
I have got to try something.
When it goes wrong the g-code stops in it's tracks along with the machine and then carries on but not in the right place or one of the X or A stepper motors takes a extra second before moving with the other one.