That's rather interesting, I wish I could furnish some insight, but that's not the case.
Let me suggest something, however, try compiling the subversion version of Pymol 1.6.0. I just compiled that yesterday evening straight 'out of the box', in Xubuntu 12.04, and it's working!!!!!
Stephen P. Molnar, Ph.D. Life is a fuzzy set
Foundation for Chemistry Stochastic and multivariate
Running Ubuntu 12.10 on an AMD64 machine, I have not been able to get the "debichem" binary version (current 1.0.3) to work, and so thought I would try a home-build of v.1.1.0. Cmake seems to find all the requisite dependencies alright, but after a lot of "make -j2" work (most not shown below), I get an opaque symbol lookup error (shown below), which confounds building the binaries.
Can anyone point me to which lib/lib-version might satisfy the missing symbol?
[ 11%] Generating moc_pythontool_p.cxx
[ 11%] Generating libavogadro_de.qm
/usr/bin/lconvert: symbol lookup error: /usr/bin/lconvert: undefined symbol: _ZN16QCoreApplicationC1ERiPPci
make: *** [libavogadro/src/libavogadro_de.qm] Error 127
make: *** [libavogadro/src/CMakeFiles/avogadro.dir/all] Error 2
make: *** Waiting for unfinished jobs....
[ 11%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/molecule.cpp.o