Check your Rom with Goodn64 it might be because of the following reason.
You have a Rom that is a Bad or Alternative Rom with a different Internal name & isn't recognised.
You can do 2 things here: to fix this problem:
Check
Paulob's "GoodN64 Bad2Good Patches" and you will also need
IPSWin 2.0 to Patch the Rom.
and see if it has your Roms name in there,
if it does then patch it to be recognised as the Good Rom version.
Leaving you to play on with no problem at all.
Or you would need to add a cheat into the blank menu for the game & then close 1964.
Then go into the root folder of 1964 & open the 1964.cht file in a text editor.
Search for your Games name:
In your case Super mario 64 Internal Name = [SUPER MARIO 64]
so search for [SUPER MARIO 64]
once you have found it copy what you need to a new blank page
now copy the Region rom codes only to it.
All Countries: ,0=0,
USA - NTSC : ,1=0,
Japan - NTSC : ,2=0,
USA & Japan NTSC: ,3=0, [In other words JU Region] IE: 1080 Snowboarding

Europe - PAL: ,4=0,
Australia - PAL: ,5=0,
France - PAL: ,6=0,
Germany - PAL: ,7=0,
[SUPER MARIO 64]
NumberOfGroups=(Amount of Cheats)
Cheats Name,1="Cheats Note",0,Code,
Cheats Name,(Region),Code,
Now once you delete all the other regions on that new page & are only left with your region you then count the number of cheats you have & put it in the NumberOfGroups=(Amount of Cheats)
you then copy that and then go back to the 1964.cht file and scroll to the very bottom where you will see the one you added earlier.
Paste the one you just copied under that one and then copy internal Name onto the one under it.
So it ends up looking like
[SUPERMARIO64]
NumberOfGroups=(Amount of Cheats)
Cheats Name,1="Cheats Note",0,Code,
Cheats Name,(Region),Code,
Now delete the one above leaving this one the only new one added.
Save As and then say ok/Yes to overwriting the file and then close.
Happy Cheating :w00t: