I took a look into the glitch that makes it rain in battle, and it appears to be an error in the Abilities section of the game. I created a INI file for PGE based on the INI for Gen 3 Suite. I'm able to open the game, edit the Pokedex, etc. Everything appears to function perfectly normal except the abilities. The only solution I can think of, if it's even possible, would be to delete the current abilities and recreate them all from scratch using PGE. However, I'm not entirely sure how you'd go about deleting the abilities that are currently in game. The only thing I can think of would be to hex edit the abilities, change them all to FF, and then use PGE to create new ones. This is all my theorizing though, I haven't tried it to see if it would even work.
EDIT:
https://imgur.com/fDSi8WZ HxD compared to INI of Gen 3 Suite
https://imgur.com/vKEuxpD PGE with error loading abilities
So I took a look at the game in HxD, and I went to the offset that Gen 3 Suite states abilities is supposed to be in is already just filled with free space. The confusing part is, even though HxD shows nothing but free space in HxD, PGE and Gen 3 Suite can see the names of the abilities when you load the rom into them.
EDIT 2:
Image wasn't displaying properly on my screen, so included the links of what I found.