Jeremy, I installed the X11-2.5.0-rc1 release from the Leopard dmg on a QuickSilver G4 and have noticed one oddity. Without rebooting yet, whenever I select the "About X11" dialog from the X11 application, which is launched when starting x windows programs, it reports...
Xquartz 2.4.0 (xorg-server 1.5.3-apple14)
Is this just a typo in the strings of this for this release? Other than this issue, pymol seems to run fine under this release without any regressions in its demos on a Radeon 9600 graphics card.
It should report: 2.5.0_rc1 (xorg-server 1.7.5) Do you have multiple X11.apps on your system that have bundle id org.x.x11? (The MacPorts one is different)? If so, it might've replaced a different one. You can check /var/log/install.log (grep for X11) to see where it may have been redirected.