I've been having the 'lost connection to server' too many times. It seemed to be fine yesterday but not today, on one of my characters 'we' couldn't finish the mission because others apparently had lost connection too.
On one occasion we couldn't finish the mission because of this; since there seemed to be at least 2 others that had the same issue.
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http://sto-forum.perfectworld.com/showthread.php?t=870691