Doesn't change much for me, I actually went the exact opposite way and I now have slightly less problems.
On the first run ffdshow asked me if it should be used in QuestViewer.exe and I answered no, never (the equivalent to adding it manually).
I later, out of desperation, changed that to always use in QuestViewer.exe and my successful launches of the game increased just a little bit. QuestViewer.exe works fine with and without ffdshow for me, but I never really had any problems with the videos anyways, only just about every other bugs out there.

I'm using beta4a of the ffdshow tryouts by the way (which can be considered the latest "stable" despite its name):
http://ffdshow-tryout.sourceforge.net/ maybe you might just want to upgrade?