I think I have the EXACT same problem. (Everything also up to date)
I can't view movies that were viewable just days ago. (So, I am guessing this happened for me with the most recent OS update a day or so ago.)
Some videos from my (non iPhone) cameras will play. But LOTS don't. Some have audio and no video. iPhone movies won't play at all.
I can't import videos from my iPhone 5 into a library -- not even a brand new library. It gives me the same message that it is an unrecognized format. In fact, I can't import .mov files from two new Canon cameras that I imported from just days ago! I get the same error message.
This happens with some variation in both Aperture and iPhoto. Actually, iPhoto shows many of my videos (except iPhone vids), unlike Aperture which lets me view very few.
I have repaired and rebuilt the library/database. As I said, I have created a new library. No change - same problem occurs.
iPhoto won't even let me export video.
But, if I view the original movie file in finder, everything works fine, no problems - I can Quick Look it, open it in Quicktime, etc. etc.
** This is THE ERROR MESSAGE that I am getting TONS of in the console whenever I try to do just about anything with movies: **
Any help greatly appreciated.