I've tried 1.7.4 and still the same issue,Why dont you try to reinstall retroarch. Delete everything and install new one fresh, maybe that will do...
I know, Kai is best gba emulator on PSP, i used to play it when i had PSP 2004, and i was happy, but for example castlevania did not ran full speed, but i beat that game wishing it ran faster (to 60fps) also i couldnt play metroid fusion properly and many other games, but they ran decent on kai. better than any other gba emulator for psp.
Than i used retroarch vba next when i bought vita and it was like a dream!
Seriously, try to reinstall retroarch to newer stable build 1.7.4
https://buildbot.libretro.com/stable/1.7.4/playstation/vita/
and I beat Metroid fusion on the kai emulator I found it ran just fine :/