I was able to somewhat fix this; instead of having a permanent options menu I used NSUI to set the options I wanted before making the .cia file (this is an injected game.)
Did you ever find a solution to this? Currently I'm having the same issues; I would love to use the VC inject for this particular rom hack (Pokemon Theta Emerald Forever) since its incredibly stable, but the day/night cycle doesn't work. The method that sort of worked was the GpSP forwarder; as...
I cannot access the Options menu in the SNEX9x bottom screen; I seem to only have access to the Game tab and the Cheats tab. I am using v1.21. How would I be able to access the options menu that allows for settings like In-Frame Palette Changes?