Comment 10 for bug 840974

Thanks for attaching the dmesg output with debugging turned on. Looking through it I do notice this bit which looks possibly complicit in this issue:

[ 515.630872] [drm:intel_prepare_page_flip], preparing flip with no unpin work?
[ 515.683339] [drm:intel_wait_for_vblank], vblank wait timed out
[ 515.683439] [drm:drm_crtc_helper_set_config],
[ 515.683445] [drm:drm_crtc_helper_set_config], [CRTC:4] [NOFB]
[ 515.683457] [drm:drm_crtc_helper_set_config], [CONNECTOR:5:LVDS-1] to [CRTC:3]
[ 515.683463] [drm:drm_crtc_helper_set_config], crtc changed, full mode switch
[ 515.683468] [drm:drm_crtc_helper_set_config], [CONNECTOR:11:VGA-1] to [NOCRTC]
[ 515.692792] [drm:intel_crtc_cursor_set],
[ 515.699776] [drm:i915_get_vblank_timestamp], crtc 1 is disabled
[ 515.716486] [drm:i915_get_vblank_timestamp], crtc 1 is disabled
[ 515.733167] [drm:i915_get_vblank_timestamp], crtc 1 is disabled
...

Those crtc 1 disabled messages go on for almost 20 seconds, so I presume this sequence corresponds to when your screen was blanked. Looks like at that point the LVDS was mapped to crtc 3; perhaps X was expecting it on crtc 1 instead and started issuing the warnings when it didn't find it there.

Would you be willing to do a quick check that this same behavior occurs in Ubuntu Precise? It should be sufficient to boot a Live USB session, configure the monitors, and see if it is working properly now. You can get the current Live USB desktop image at http://cdimage.ubuntu.com/daily-live/current/ and create a USB boot drive using usb-creator.