there is something strange with the axes and the bounding box.
To see what happens, open bulk_Si.in, select Axes and bounding box in preferences. Then open Crystal Properties and change the representation from Cartesian to Crystallographic (in the first panel). Click Apply.
The crystal is still correct but the bounding box is now different. This is no more a cube but a rectangle parallelepiped.
Should we worry about that or can it be considered normal?