on a slightly different subject, why are you rendering as jpgs? jpgs are a lossy compression and thus you will have artifacts in your render. Why dont you render as tiffs or targas? that way a you will get an alpha channel and b you will have lossless compression on the files. Oh and you should always pad with at least 4 figures not 3
As for it defaulting to iff's I'm not sure. There are certain things in maya that can only be done with iff's such as z depths etc but that shouldnt be a problem.... hmm could you post a scene file where you're having the problem?
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