I have used Vortex many times before. And most times without problems but after finally getting VR, things arent working as planned. I have the mod staging folder and game folder on the same drive but whenever I try to deploy mods it doesnt put the mods into the game and will say they are redundant. Even if its just one mod enabled it still is redundant. Any help?

Try reinstalling your mods. Then verify that they appear under StreamingAssets/Mods in the game folder :)