Hi Mones!
In order to fix this issue you need to select a different standard shift to the origin option. In the third line of the input, where is normal to include three zeros, you should change the last zero to one (like this: 0 0 1). As stated in the manual, this will select the first setting for the shift as available according to the International Tables. As far as I know, the best way to know when you need to use this option is to always initially perform a geometry test (TESTGEOM keyword), visualize the system, and consider this change from 0 to 1 as a possible solution if the rest of the geometrical data (space group, cell parameters) are consistent with your expected system.
I'm attaching back the input including this change (tppvo1_fm_fullopt.d12). An initial test run seems to indicate you might also need additional instructions in order to correctly handle the system's symmetry along with the spin configuration you are trying to use. For this, refer to the manual (ATOMSPIN keyword, page 99): the current output (tppvo1_fm_fullopt.out) will give you some hint in how you should modify the symmetry of your system (MODISYMM keyword) in order to use your current spin configuration. Or if you don't want to keep any symmetry operation, you might as well remove all of it (SYMMREMO keyword). I might suggest to post another issue if you have further problems with this.
Let me know if this solves you current problem, as well as any further question