This is happening to me now, it worked fine in the beta, then i went back to 13.15 and just installing 13.16 only shows when selecting for some games.
EDIT: Maybe it wasnt picking up everything before and i just hadn't noticed.
Also i've added batman beyond PS1 yesterday (not played) and its showing the same save as N64 version.
EDIT 2: Im using Retroarch 1.15 and sort saves and save states to folders with core name was off, maybe the default has changed on the latest version (i don't know why i would have turned that off.)