@mitu welp, you solved my problem. So emulationstation if launched from c:\programfiles\emulationstation\emulationstation.exe it is v2.9.0RP-DEV which works fine. I originally set it to install in D:\emulationstation so the exe in that location launches v2.0.1A which I just realized I accidentally deleted my desktop exe and then went to that location to grab it again. Dont know why there are 2 locations but v2.0.1A is what causes a problem. Somehow when typing this I went to 2.9.0 without thinking to check the version and then just closed it but every time I tried to use a controller I was launching v2.0.1. Sorry and thank you ._.
Going to leave this up unless mods wanna delete it cause maybe others might make a dumb mistake like me.