Hi Jason,
I think you might have fixed it.
It is difficult for me to tell, because I ported my larger roms (wii, gamecube etc) onto a different drive today, which for some reason seemed to eliminate 90% of the xinput lag I was experiencing. However, I think I was still seeing lag after closing a game, compared to the keyboard.
I've got 8.6 beta 1 up and running and I don't see any controller lag now. So.. maybe fixed in my instance?
Thanks for your efforts.