When I try to use 1964 with OoT I now get a "Exception happens during boot" error which is followed by an illegal operation. Under comments in the 1964 rom browser, zelda wasn't down as playable so I went to zophar for a new ini but that didn't help. It probably has to do with it being version 1.2.
It seems if I try to play any other game I get a eeprom loading error or "unable to create new mempak file" error with an illegal operation.
I found another member on this board which has the same problem as I do with project 64 and OoT
here but they don't have a fix or an understanding of why either.