Ah, i had the same problem at first but i found out what it was. im not really sure if i can post it here but...this could solve your problem.
10. No$GBA Snapshots (save states)?
These only work for GBA games at this stage.
why does it restart? because it still not suited for NDS games yet, and can't read the file.
i hope that solve your problem.
If that's not the case...
I been playin "Rune Factory 2" for a while and there seems to be no problem with it. But the program i use is "No$Zoomer 18.104.22.168
" to play it. It require No$gba2.6a since it the same but has the plugin to play most nds games now.