OK, this is what is happening on my machine when I reproduce this:
1) I insert a USB Flash Drive that has a duplicate UUID as one of my hard 
drive's partitions.
2) udev changes the symlink /dev/disks/by-uuid/<duplicate UUID> to point to the 
Flash Drive's partition.
3) GParted checks /proc/mounts to determine which partitions are mounted.  
Since the original /dev/disks/by-uuid/<duplicate UUID> is actually mounted, 
GParted doesn't know any better and flags the USB Flash Drive partition as 
being mounted.

Unfortunately, I'm not sure if there is a way to really fix this.  The
udev developers believe that udev is behaving as expected - having
multiple partitions with the same UUID can lead to unexpected behavior.

Dallman, you can probably work around this issue by changing how Ubuntu
mounts your root partition.  If you edit /boot/grub/menu.list, find the
line that says kopt=root=UUID=<my UUID>.  Replace the UUID=<my UUID>
with /dev/<root partition>, e.g., /dev/sda7.  Then run 'grub-update'.
After rebooting, /proc/mounts will contain /dev/sdaX, rather than
/dev/disks/by-uuid/<UUID>.  GParted won't see the cloned partition as
mounted anymore.

-- 
gparted wrongly reports partition "mounted" when uuid and label are duplicates
https://bugs.launchpad.net/bugs/579703
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