The libraries are processed, specified isotopes are read in and any part of the cross section tables that are not needed for the problem are removed. Memory is reallocated for this process. An error in the library, or an out of date or too new library, can break things.
It might be worth doing md5sum on the library directory and see the sums differ from known good copies. Most of the libraries for MCNP/X are now freely available, which might help.
It's possible the data path is wrong, but it is finding the libraries so that seems to be working.
It's possible it could be an xsdir file error, but I wouldn't know how to check this. If you have other versions, you could try those.
You could see if it only affects some problems or some isotope materials. You could try explicitly specifying certain libraries.
I wish I could be more specific, sorry, but good luck!