As far as I can recall, nothing was modified in AlphaSim for a long period of time.
A couple of things you can check:
(1) Is the mask
auto.mask.di3.obs.012+orig still the same as before?
(2) In your script
AlphaSim -nx 64 -ny 64 -nz 29 -dx 3.75 -dy 3.75 -dz 5.00 -iter 1000 -rmm 5.2 -pthr 9e-06 -fwhmx 23.11 -fwhmy 27.63 -fwhmz 20.58 -mask auto.mask.di3.obs.012+orig. -out Significant9e-06rad5.2.with.fwhm.and.mask, it seems
-nx 64 -ny 64 -nz 29 -dx 3.75 -dy 3.75 -dz 5.00 is redundant (or conflicting?) because the program can get dimensions and voxel resolution from your mask.
Gang