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@will
You are right that LaTeX by default will not hyphenate already hyphenated words. However, as always, there is a package to correct this behavior: hyphenat.sty
Holy crap, that's pretty cool, thanks. I wish I'd known about it three months ago. :-)
For anyone who's still checking: Wolfram (the developers of Mathematica) have got their own publishing package for scientific writing now, which I think interfaces with TeX. It's called Publicon, and you can try it for free. Unfortunately, they didn't pay me to mention it :-( and I forgot to try it during the trial period after I downloaded it. So could someone try it & let me know how it is? :-)
http://www.wolfram.com/products/publicon/index.html