Which is the example given in the XMakemol Documentation.
The creation of the crystal is impeccable, however when you save the crystal for another file, or overwrite the original one, the result of the new saved file (no need for it to be changed, may be everything as original file) will be something like this:
Na 0.000000 0.000000 0.000000
Cl 2.500000 2.500000 2.500000
As you can see the saved file loses the crystal periodicity, and from then on is just 2 atoms... I don't know which would be more useful, keeping the crystal periodicity (which can be kind of hard to determine after some translations, rotations, inversions and reflections have been made) or saving only the positions of the atoms that are being shown (for the example above the 25 atoms of Cl and the 25 atoms of Na), which can be easily done (at least more easily than maintaining the crystal structure, in my opinion).
I don't know if this bug has not been already corrected, I've found it a couple of months ago.