I think that when this happened I had recently invoked spaces to check my calendar and when I returned to the X11 space things were all messed up. I wasn't able to go through the debug steps Jeremy outlined below (sorry about that) but I do have the tail end of the /tmp/quartz-wm.log file to share:
x-input.m:x_input_run:918 <Unknown:69 window:0>
x-input.m:x_event_apple_wm_notify:808 kind IsActive arg 0
x-input.m:x_input_run:918 <Unknown:69 window:0>
x-input.m:x_event_apple_wm_notify:808 kind IsActive arg 0
x-window.m:-[x_window decorate_rect:]:1013 TRACE: 60003c
x-input.m:x_input_run:918 <ConfigureNotify window:681>
x-window.m:-[x_window report_frame_size:]:663 TRACE: 60003c
x-input.m:x_input_run:918 <PropertyNotify window:100001f>
x-input.m:x_input_run:918 <PropertyNotify window:100001f>
x-input.m:x_input_run:918 <PropertyNotify window:100001f>
x-input.m:x_input_run:918 <PropertyNotify window:100001f>
dock-support.m:dock_message_handler:91 <DockMessage id:1 wid:3821
x-window.m:-[x_window activate:]:1709 TRACE: 100001f
x-window.m:-[x_window show]:1699 TRACE: 100001f
x-window.m:-[x_window focus:raise:force:]:1625 TRACE: 100001f
x-input.m:x_input_run:918 <ConfigureNotify window:681>
x-window.m:-[x_window report_frame_size:]:663 TRACE: 100001f
x-input.m:x_input_run:918 <FocusOut window:400013>
x-window.m:-[x_window x_focus_out]:1739 TRACE: 60003c
x-window.m:-[x_window decorate_rect:]:1013 TRACE: 60003c
x-input.m:x_input_run:918 <FocusIn window:400020>
x-window.m:-[x_window x_focus_in]:1722 TRACE: 100001f
x-window.m:-[x_window decorate_rect:]:1013 TRACE: 100001f
x-input.m:x_input_run:918 <Unknown:69 window:0>
x-input.m:x_event_apple_wm_notify:808 kind IsActive arg 0
x-input.m:x_input_run:918 <ColormapNotify window:60003c>
x-input.m:x_input_run:918 <ColormapNotify window:a00367>
x-input.m:x_input_run:918 <ColormapNotify window:a0063b>
x-input.m:x_input_run:918 <ColormapNotify window:a0086a>
x-input.m:x_input_run:918 <ColormapNotify window:a00869>
x-input.m:x_input_run:918 <ColormapNotify window:a00836>
x-input.m:x_input_run:918 <ColormapNotify window:120001c>
x-input.m:x_input_run:918 <ColormapNotify window:a006f4>
x-input.m:x_input_run:918 <ColormapNotify window:a00033>
x-input.m:x_input_run:918 <ColormapNotify window:100001f>
x-input.m:x_input_run:918 <Unknown:69 window:0>
x-input.m:x_event_apple_wm_notify:808 kind IsInactive arg 0
x-window.m:-[x_window decorate_rect:]:1013 TRACE: 100001f
x-input.m:x_input_run:918 <FocusOut window:400020>
x-window.m:-[x_window x_focus_out]:1739 TRACE: 100001f
x-input.m:x_input_run:918 <Unknown:69 window:0>
x-input.m:x_event_apple_wm_notify:808 kind IsActive arg 0
x-input.m:x_input_run:918 <PropertyNotify window:100001f>
x-window.m:-[x_window decorate_rect:]:1013 TRACE: 100001f
x-window.m:-[x_window focus:raise:force:]:1625 TRACE: 100001f
x-input.m:x_input_run:918 <FocusIn window:400020>
x-window.m:-[x_window x_focus_in]:1722 TRACE: 100001f
x-input.m:x_input_run:918 <PropertyNotify window:100001f>
x-input.m:x_input_run:918 <Unknown:69 window:0>
x-input.m:x_event_apple_wm_notify:808 kind IsInactive arg 0
x-window.m:-[x_window decorate_rect:]:1013 TRACE: 100001f
x-input.m:x_input_run:918 <FocusOut window:400020>
x-window.m:-[x_window x_focus_out]:1739 TRACE: 100001f
x-input.m:x_input_run:918 <Unknown:69 window:0>
x-input.m:x_event_apple_wm_notify:808 kind IsActive arg 0
x-input.m:x_input_run:918 <PropertyNotify window:100001f>
x-window.m:-[x_window decorate_rect:]:1013 TRACE: 100001f
x-window.m:-[x_window focus:raise:force:]:1625 TRACE: 100001f
x-input.m:x_input_run:918 <FocusIn window:400020>
x-window.m:-[x_window x_focus_in]:1722 TRACE: 100001f
x-input.m:x_input_run:918 <PropertyNotify window:100001f>
x-input.m:x_input_run:918 <Unknown:69 window:0>
x-input.m:x_event_apple_wm_notify:808 kind IsInactive arg 0
x-window.m:-[x_window decorate_rect:]:1013 TRACE: 100001f
x-input.m:x_input_run:918 <FocusOut window:400020>
x-window.m:-[x_window x_focus_out]:1739 TRACE: 100001f