There were some discussion on the VMD list about threading stability problems on recent linux versions, and the same issue now seems to be affecting PyMOL. If you enounter such problems, then you may want to try setting the LD_ASSUME_KERNEL to 2.4.20 as a workaround before launching PyMOL.
bash: export LD_ASSUME_KERNEL=2.4.20 csh: setenv LD_ASSUME_KERNEL 2.4.20
