I can't think of any reason the audio would get bigger.. PDA is PCM data just like WAV--in fact, for 16-bit data the only difference between the two is the header. I'd be happy to take a look at your files if you'd like, try and figure out what's blowing up. Also, if you've got a mac you might have better luck with the encoder app: Video encoder (work in progress, mac only) - #23 by dave I still haven't gotten a portable command-line version running yet, but I'm working in that general area right now so hopefully I'll be able to pay that some attention soon.
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