Amada Pega 244 A/I delay issue

Hi there, having problems with the auto index drives on our amada pega 244,.
The index pins are out when the machine is off.
They engage when started.
So I am assuming that the switches actually work
I can not release them when I toggle the Index Pin switch.
The error appeared about 20 seconds into the punching cycle.
It was an A/I station in use at the time.
All fuses look ok and so does the A/I

We can still run programs but have to leave the auto index tool until last.
It has to be a program issue we have looked over it mechanically, and checked the internal resistance in the proxi switches which all seem to be fine.
We have swapped the control relay for the air solenoid that releases the drives also not fixing or changing the issue.
It is exactly 20sec between the request to retract and the fault, which must be watch dog timer, however when the machine does it's index when first turned on it this drive shaft system works fine.
Thanks in advance for any help.