I have this issue of my camera (Nikon D7100) randomly stopping in the process of shooting a stack. Sometimes it goes trough all of the steps but most of the time it just stops on the first, third, fifth or for example eighth shot. When I try to stop the proccess of shooting after it stops, programe doesn't reply, it's not completly frozen but it does'nt really react either. I have to turn off and on my camera, reconnect it to the computer and start all over again.
Somebody described the same issue somewhere, years ago and allegedly turning off live view while shooting worked, but not for me
Thanks for any helpfull reply