I have previously noticed my longer running uploads using GWT may have an hour where no uploads were happening, and put this down to operational queue priorities. In the last day upload queues appear to be not re-scheduling but have been on indefinite wait, this is not due to upload failures as the queues can be forces to temporarily restart when a new upload tranche is added.
As it is not possible as an end user to see what is going on with queues, users will automatically assume that uploads have either completed or fallen over. Gaps of several hours or days are likely to result in duplicate upload runs, or (as I have done here) just having more queues added by accident without waiting for the last to actually complete.
History from my uploads for the Historic American Buildings Survey project ( see http://commons.wikimedia.org/w/index.php?title=Special%3AListFiles&limit=250&user=F%C3%A6 ):
06:26, 23 July 2014 - 10:33, 23 July 2014 (4 hour gap)
Temporarily restarting with a new queue was added.
10:34, 23 July 2014 - 15:00, 23 July 2014 (4.5 hour gap)
Temporarily restarting with a new queue (1801:2000).
16:36, 23 July 2014 - 06:22, 24 July 2014
Another temporary restart when adding (2001:2300), however files from the last two upload tranches can be seen at this restart time.
06:23, 24 July 2014 - [Current time, 13:02 in UK, 6.5 hours and waiting]
There should be around 15,000 images on queue at this point, so I'm avoiding sending off another tranche until we know what is happening.