I've discovered that the latest version of Doxygen (1.3.8) gives doxygen2boostbook fits. If you're on an earlier version that is working for you, best to stick with it until the problem is fixed.
If you need a version of Doxygen that works with boostbook, find version 1.3.7 for your platform at ftp://ftp.stack.nl/pub/users/dimitri/. I've confirmed that that version works fine.
-- Eric Niebler Boost Consulting www.boost-consulting.com
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