Try a reboot while holding the shift key. This will boot you to safem mode. Safe mode stops all startup and launch items from running. If the problem goes away in safe mode, that tells you you have a launch item or startup item that is conflicting with El Capitan.
If safe mode fixes it, post back here and I can suggest some ideas for troubleshooting.
Aw, that does not look good. Can you isolate it to a particular app? It might be a buggy app that creates too many graphical resources (which then end up being managed by the window server).