Fail to homing (mechanical switch + index pulse)

What did you upgrade? Linux or LinuxCNC?

(And from what to what)

What does uname -a now say?

And is there a message when it crashes?

The (partially) good news is that you haven't upgraded the OS and lost the realtime kernel in the process.
(Though that would be an easy fix)

Moving from LinuxCNC 2.7.12 to 2.7.13 ought to make things better, not worse.

It is possible that some other package has been updated and that is causing an instability.
looking in the /var/log/apt/history.log file might show what else was updated at the same time.

I found it through a Google search (I am not on a Linux machine at the moment)

Google also suggests opening the Synaptic package manager and looking in File -> History.

CNCCustoms wrote:

Ok Thanks Andy... I will check it out. Any luck on the index homing issue?

I think the problem is likely to be that the feedback is coming from the stepgen and not from the encoder.

I think with a velocity-mode stepper system using PID and encoders with index the position feedback needs to come from the encoder.
I am unclear whether all the feedbacks need to be from the encoder, but the PID certainly does.