Make sure you have a nand dump from a real 3DS in your user folder.
Check this site to see what the folder layout should look like.
https://citra-emu.org/wiki/Home-Folder
Thanks for the reply, although it turned out that it was indeed a GFX Card Driver issue. I knew my drivers weren't up-to-date, but they were far more outdated than I thought, yet all my pc games are working just fine, so it didn't immediately cross my mind.
Both Pokémon X and Omega Ruby aren't running half bad I have to say; Fps is certainly jumpy in some locations, but they both seem to run decently.
Alright, I got to test the games properly which is what I wanted, I'm satisfied for now Thanks for the replies guys.