My method to build the pgfmanual.pdf is :
$ cvs -z3 -d:pserver:anonymous@pgf.cvs.sourceforge.net:/cvsroot/pgf co -P pgf
$ cd ~/pgf/doc/generic/pgf/version-for-pdftex/en
$ mkdir plots
$ TEXINPUTS=".:~/pgf//:" make
$ TEXINPUTS=".:~/pgf//:" make dist
$ TEXINPUTS=".:~/pgf//:" make dist
$ cd ~/pgf/generic/pgf/testsuite/mathtest
$ pdflatex mathtest
$ cd ~
$ make -f pgf/scripts/pgf/Makefile.pgf_release
The result is correct. Automatic cross references in codeexamples are enabled, the links work but I lost the blue color for these links. The pgfmanual-pdftex.cfg file is unchanged . I work with MacTeX 2011 prerelease and pdflatex.
I put the files here