there is a default value which determines how far from the atoms the data for the orbital shall be calculated. If your value for the iso-surface is too small, you will sooner or later hit the limit.
Try to increase the value at which the orbital is being plotted until it fits in the box.
Or increase the 3D grid size - but for that you have to switch to the command line. Add
$pointval mo <mo-number>
grid1 vector 1 0 0 range -4,4 points 300
grid2 vector 0 1 0 range -7,5 points 300
grid3 vector 0 0 1 range -5,5 points 300
to the control file. Change the range and the number of points according to your needs.
Then run write_plv or either dscf -proper or ridft -proper to get the .plt file which TmoleX can visualize.