sheson and EssArrBee, thankyou for your quick responses! It seems Google let me down, and I was looking at things entirely wrong. Adding;
[Archive]
sResourceArchiveList=Skyrim - Misc.bsa, Skyrim - Shaders.bsa, Skyrim - Textures.bsa, Skyrim - Interface.bsa, Skyrim - Animations.bsa, Skyrim - Meshes.bsa, Skyrim - Sounds.bsaas you suggested to my skyrim.ini seems to have resolved the issue. However, I'm curious as to what went wrong, as it seems like Mod Organiser should have been loading those bsa files already: