I solved my own issue, thankfully, after four days of constantly trying. No help from here, sadly.
I went into my folder where I kept the mods and wondered if somehow the game was still picking up my package file outside of the main game/patch directory. I deleted it and now I no longer have the issue. I hope that helps someone else. Despite having removed the game, downloading it again and patching it with a vanilla patch, it was still picking up a package file from elsewhere. Even though I had not run the mod manager with a fresh install it must have been mucking things up.
I hope this helps someone who is having issues with war table quests not appearing.
