Would it be possible to export that substance with dependencies, and share it with us (either post it here or by private message), so that we can investigate further ? Otherwise it is probably going to be impossible to reproduce that particular bug on our end.
Regarding the fact that the SD process does not close, are you running SD from Steam, or is it a standalone SD installation ? Also, where was located the sbs file you were working on (in Desktop, in Documents, in Temp, on an external drive, on a network drive, etc.) ?
Thanks.