I have a similar issue with the mkv video format and certain apps, if the file is in GoodReader or similar and I use the open in feature, the registered media apps will not show up. This is on my iPad 2. The weird thing is with the exact same set up on my iPad 1, the media apps do show up as possible destinations. I worked with one of the media app devs and we were unable to get to the bottom of this. It seems like the app registration for the open in feature is a little flaky.