@Miguel_Sanchez
LinuxCNC is an extremely high reliability software suite. That being the case the odds of you running into a show stopping bug running it are exceedingly low too. Well, a bug that you didn’t have a hand in yourself creating that is.
In the end, as it was expected, LinuxCNC was not blame but the parallel port configuration, that will cause X-axis to stop working for a while every now and then. Replacing the computer cured the problem (maybe it was just bad BIOS setup of parallel port).