In your log file there is a message: "Runway RW13 not found at airport KMLS but it is necessary to build procedures. Missing runways should be reported to the scenery gateway". Did a window also popup asking you to click on a button to report the missing runway? The other, technical problem popup "bid_EUapart1_ALB.png" in default scenery. There was nothing in your log about that, only about missing runway RW13. So if it was the missing runway that shutdown the updater, more likely, or "bid_EUapart1_ALB.png", not mentioned in the log. If you got no popup window about missing runway, to report it, then that is probably the reason for the shutdown. I would report both, if there was no popup window to report missing runway, or just the "bid_EUapart1_ALB.png" message, as a bug causing the updater to abort, in the bug report page or "contact support here" link, on the same page.
http://dev.x-plane.com/support/bugreport.html