Same when one would build by using the cbp's files. Then you actually don't know what bootstrap/configure is ;-), you build and call update.
when "make" or "pressing build button" in CB is not sufficient to build (when no new plug-ins,libraries are added), plain simple : build system is wrong.
The difference is that the ./configure handles many systems and handles dependencies, C::B's build system doesn't.
I don't know what has happened on your system, probably some dependencies are not handled. If you can reproduce the problem we can try to fix it.
Probably update back to r7920, do a full clean build, update again and do another build with make only.
Also keep in mind that make uninstall is pretty useless...
I generally follow the boostrap/configure/make/make install command chain, when I want create installable versions of C::B and I have no problems.
I do this in order to get a reliable version of C::B.
And after an update I always do a full rebuild even using C::B's build system, just in case.
Another thing, it is always better to build packages for the distribution you're on instead of using make/make install directly.
I do this both on gentoo (where I have an svn ebuild) and on centos(where I use rpmbuild to build rpms).
I guess Jens could post the steps needed to build debian packages.
This is the most reliable way to install software on linux. If you don't like it use windows or macosx (the drag and drop territory).
p.s. you reminded me that I've forgotten to fix the Makefile.am in my last commit...