1. Nands are linked. When I first set up emunand, I formated sysnand, but they were still linked... (multiple signs showed this)
2. Menuhax: I have it on sysnand, I have it setup so that I'm required to press Up+B to load it, and have always ran it that way. Because you mentioned that, I did try launching emunand while holding the default and my custom menuhax launch combinations. Still shuts down.
3. Oh yeah, I didn't say that I installed the patched AGB_FIRM, my bad XD (Pokemon Sapphire actually ran, so I know that that part worked.)
4. 2.5, I know I need to update, but I've just been way too busy to do it. But I installed FBI in sysnand through the rxmenu, then in devmode sysnand I'm able to run the GBA games and FBI, but when in plain sysnand it just says "reinstall this app from eshop".
So yeah... am I fucked because I'm on an old rxtools? Or do you think there's still hope?
[Edit]
Forgot to answer this: No, I haven't tried updating through sys settings because I know my nands are linked, and I know that I could easily screw everything up that way.