You know, that could have been what was happening to me. I never had any cutting out sound (I don't think) or anything like that, but the game would freeze and I couldn't get past one cut scene (which was like 10 min. into a mission so I only tried twice).
Yep, sounds like you got the same issue -- in-game sound is perfect, but the FMV's play TOO slow w/ the sound.
Before you do the sound unpacking thing, you can try a few things to avoid this -- since you'll have to do a lot of steps and a lot of waiting to unpack 3 GB of sounds; some file cut & pasting; and a handful of "Ambient sound" renaming.
Try the Call of Duty 5 PC, Call of Juarez: Bound In Blood PC work-around first. Switch your Sound Card Program's settings (i.e. use RealTek Manager, if you have a RealTek card) -- especially if you're on Windows XP -- and set it to 44.1 Khz. Or, if you're on Vista or above, you can do one better and go through Windows and be precise and switch them to 44.1 Khz setting. Run the game, see if it goes well. If so, great!
If not, ugh! Let's try some other things.
If you have to, jump into DirectX and set your Sound Acceleration at any setting BELOW Full. Work from right to left. Try every notch UNTIL you run into one that works OR you run out of settings.
Another thing to try -- swap out BinkW32.DLL with a newer version of itself. Find a game that you have that has a NEWER version of BinkW32.DLL than Prototype's (i.e. see Wolfenstein 2009 or Section 8 ) -- or see if you can find it uploaded online somewhere. Just rename Prototype's BinkW32.DLL just in case you might need it again for back-up purposes, if necessary -- rename this old one to BinkW32_old.DLL (or whatever your soul feels content to doing). Move your newer version of BinkW32.DLL from some other game (like say Wolfenstein 2009 or Section 8 ) into the same exact folder as Prototype's BinkW32_old.DLL.