When FNV starts it turns on FFDshow audio decoder. Any reason why its using it?

if you installed mpc or cccp codec packs (or any of the half dozen others) you'll have to manually set ffdshow to ask if it can be used with an application. best answer is no, not allowed to be used with any game. at a guess it's bink that it's loading for (intro vids, in game vids). can't tell you specifics as your install may differ, check google for how to disable ffdshow from running with fnv.

why disable? because unless beth is unique and supports ffdshows decoders no game is made to use it.

It really shouldn't. You should go to the config utility for ffdshow at once and add the .exe to the exceptions. Games with Beth's engines have major problems with some third party codecs.