it will be that issue I mentioned before
The folders are udata and tdata one has saves in the other has game data needed to start certain apps and for one reason or another the xbox limits how many of those are created and cant create new ones once that limit is reached
to solve that temp move those from the xbox via FTP or move them to a new folder via one of the many on system file managers
run the software that is failing the newer N64 emu and coinops running the N64 games and see if that works
after you done that once you can restore the udata and tdata folders
The folders are usually in the root of E:\
That problem is known with games from both disc and installed, the limit is on creating not reading though so that problem will keep coming back with every new piece of software used that you have not had on there before
New versions of software usually would not be an issue unless they changed the default ID for the software so when it creates the files in the udata and tdata folders it has to make a new folder/files and without being able to create those you just get a black screen
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