@tuxor: Don't know whether the issue is still open, but later on I found out that build creates some configuration files in the build/... subdirectories that were not always updated. So deleting the respective subdirectory solved the issue for me.
Moreover I noticed that dependency handling seems to be a sensitive issue on amd_64 machines... e.g. the libz issue just disappeared in a 32bit Ubuntu lucid environment (without applied patches - which are required for the 64bit lucid).
I'd therefore suggest developing in a 32bit virtual machine (I grabbed the one Nokia offered for N900 development, which I also used for the Iliad

)
W.r.t. the from-scratch-against-onyx-scribble discussion: An advantage to modifying that one would be that the extensions would be available for PDF annotations as well (e.g., I dearly miss different colors :P).
But I can also understand why one would rather want to write things from scratch than patch undocumented code

.
Cheers!