Hello Sarto
Honestly, I have not faced this problem so far. But what I have done was with the latest version of STaMPS (4.2.B) and snap(7). I know that for older versions of stamps you have to replace two files that are associated with MATLAB with the adjusted versions of those files. Nothing seems wrong to me in this step. Just be sure that the MATLAB is working properly in Linux. then another point is when you see an unsuccessful process, delete the temporary files and then do mt_prep_snap again.
It is also possbile that something is wrong with the initial process in SNAP, recheck everything and try to use different combination of SAR images or different siz of substract.
I check the error and I saw that another guy named MARCU had the same problem, however, I coulnd find any update to see what he have done to overcome it
and take a look at this instruction by Thorsten, although it is for older versions, it is much more in details
snap_stamps_1_0.zip (2.1 MB)
Finally, don’t worry. in different systems, weird stuff might happen. But I am sure you can find the errore