Go into the No$GBA options and ensure the correct save type has been selected. If one does not work, keep trying until you find one that does work. Remember, these vary between games ,but with 2.6a the Auto option should work fine. The name of the setting you should be looking for is NDS Backup Media Catridge.
rune factory is playable on no$gba 2.6a just make sure that under gba mode, in emulation setup, is on vga (poppy bright), then when you click or hit enter or anything the game will continue normally.
EDIT - ok ive reexamined my settings multiple times and so far the game working seems to be a random thing so as of right now its like if your willing to press the star on your num pad everytime you load it up to reset it and use the + on your num pad to speed thru the intro to the opening vide and press the a button untill it works then ya get it but till i or sumone else can figure out how to make it a always work thing then forget it lol but ima continue trying to make it work