HI Kyle. I'm having the same problem. Did you ever figure out a solution?
Sorry not yet... we just went to a different codec for outputting. But i would still love to know what happened to the DV codec if anyone can explain?
In previous versions of After Effects, the imprecise names of the codecs as supplied by QuickTime were used. In After Effects CS5, the more precise names of the codecs are presented in the UI. For example, 'DV25' is what is usually meant when people say 'DV codec', even though it's just one of many DV codecs.
This is also being discussed on this thread: