This happens in both ZC Beta 178 and 163.
There is one particular room in Level 3 of Nightmare's James Quest 2 that, whenever you go into it, Zelda Classic immediately exits to Windows. There's no error message of any kind, just a clean exit.
I'm trying to get ahold of Nightmare so he can open up the quest and give me as many details as possible about the room where this happens. Until then there's really not much else I can say.
Dark Nation, if you want to take a look at the quest I have it available for download here. The room in question is one room down and one room to the right from the upper-left corner of Level 3.
EDIT: Nightmare gave me the password to the quest and I think I found the problem. Apparently the crash was caused by using the "has ring leader" enemy flag in a room with Lanmolas (it was a blue lanmola and a red lanmola in that order in the enemy list, and no other enemies).