Fail to homing (mechanical switch + index pulse)

What does uname -a now say?

And is there a message when it crashes?

Uname -a??

No message when it crashes. Jist freezes. Also no messages when it disables.

Ok. Uname -a says:
Linux debian 3.4.9-rtai-686-pae #1 SMP PREEMPT Debian 3.4.55-4linuxcnc i686 GNU/ Linux

Im on Gmoccapy 1.5.9

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.

That files is empty

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.