Hitchi Seiki VK 45 II keeps crashing on tool change

Hello ,

Every time after power up and axis references my machines loses about 6 mm in the x axis , meaning that if I attend a tool change the machine has a default position of X - 500.mm for the table to go to but it only reaches about X - 495 and it crashes the table with a bang, clearly it goes beyond any limit switches. Of course after that it promts E stop from the machine and X axis overcurrent alarm.
The machine sees the soft limit switches in the + or - if I jog the axis witch is ironic. The same is true about part origin , it s clearly offsetted in the x axis.
I have to restart the machine and go over the entire process about 10 or 15 times before a successful tool change and no more offset in the X axis. Then is ok for the rest of the day until the next power off
From what I see the machine has only one limit switch in the X axis mounted in the middle of the travel , the other switches are stored in software.
As a side note it started happening accouple of months ago but it took about 3 restarts to get it to work , now it takes an hour after every power up to get it working.

Any help would be greatly appreciated

Thanks