Moved form using Doxygen 1.7.1 (comes with Debian 6) to Doxygen 1.8.4 (build from sources) for the lzoDSO firmware documentation. Looks much nicer.
Still, there is a problem with the documentation (unrelated to doxygen). All code that is linked to the project repository using svn:externals properties is somehow not covered (still investigating). I think this is somehow related to the way the Bitten slave (build slave of my CI setup) does the automated build (in which doxygen gets executed).
If you ever had something similar, please let me know (via comment or Twitter).