These "isn't long enough" messages are caused by the .sdat files written during the 3dttest++ randomization runs being truncated somehow. Not empty and not non-existent, because those are different messages.

But how that file truncation happened, I don't understand. The only thing I can think of is that the disk storage is full, but that seems very unlikely, and you would almost certainly have a whole host of other messages in that situation. Although the program has many error messages built in, most of them have never been actually seen in practice -- including these "isn't long enough" messages.

Do you have the .sdat files saved? How big are they? How many voxels in your mask? The files should be exactly 2*number of mask voxels long -- the 's' means 'short' and these files are 'short integers' = 16 bit = 2 byte values.