Any other PC players having trouble with controllers occasionally dropping inputs?

[Imoen]

Device manager > Software Devices > Microsoft Device Association Root Enumerator

Disable it. This, in all my years of playing, is the only single thing that has stopped the random drop behavior, for this game. Across multiple machines, both wired and wireless/bluetooth and many different controllers.

But you said you already tried that.. so idk sorry.

Edit: The behavior was exactly the same as what you had described though. Random drop outs for a sec or two.