Single pair results are ok, but "stack results" are mistaken, so I have given up using the suggested workflow between Snap and StaMPS.
I'm not expert of cygwin and windows: I use only ubuntu.
I don't undestand well what is your problem, however, if you don't able to run stamps in matlab after mt_prep, i think the problem is that matlab don't find stamps functions. So, You could add path of stamps function to your work directory (for example in ubuntu addpath('/home/annamariaStaMPSv3.3b1/matlab') ) and it would run.
My laptop has 1Tb of hard disk, Intel® Core™ i7-7700HQ CPU @ 2.80GHz × 8 , Ram 16Gb.