Canola, AFAIK, has never had a battery problem when not in use; I'm not sure how it compares for battery drain when active.

The built-in player, OTOH, only sees your files automatically if you run a service called metalayer-crawler, which crawls through your filesystem looking for music files to index. This crawler, unfortunately, has a tendency to go berserk and consume 100% CPU, killing the battery life. Sometimes this is the result of the user's actions, sometimes not.

The safest course of action is to dump the built-in media player for most things, or at least not rely on it auto-indexing things, and disable metalayer-crawler.

Since you haven't told us what applications you can't see, we're left to guess and take shots in the dark; that's unlikely to provide you with much help...

But...
<dark>Bang!
Sometimes the menu doesn't get updated immediately, and sometimes items get inserted out of order. It's a little extreme and not necessary (it will update eventually if this is the problem), but you can reboot the tablet, then scroll all the way down the list; see if anything shows up.
</dark>

(BTW, you're having codec woes; Canola has the benefit of being able to use both the standard media-player engine, and mplayer (a different, and generally better, engine) for playing different files. That might help, and mplayer generally does much better with most stuff, though there are instances of files that work better with the standard engine. If you just want to try if mplayer works on your wmv, install it and try; it comes with its own front-end, though that's nowhere near as friendly as Canola.)