You should not worry about this too much.
Maybe your USB pendrive is of "lower quality".
The dialog output regarding the time is misleading.
Other copy tools may have a different output behavior,
but they do not improve the writing speed of the USB drive.
Most important of all is that finally the copy action succeeds.
What you can do is optimizing the input/output schedulers of disks.
Install gksu
(when you haven't already) to edit files with gedit
as root :
sudo apt-get install gksu
Now optimize the priority of all running processes for various disks types :
gksudo gedit /etc/udev/rules.d/60-schedulers.rules
Paste the following lines into this empty file and save the file afterwards :
# set cfq scheduler for rotating disks
ACTION=="add|change", KERNEL=="sd[a-z]", ATTR{queue/rotational}=="1", ATTR{queue/scheduler}="cfq"
# set deadline scheduler for non-rotating disks
ACTION=="add|change", KERNEL=="sd[a-z]", ATTR{queue/rotational}=="0", ATTR{queue/scheduler}="deadline"
The changes you made take effect after a restart of the operating system.
Also ... an alternative copy solution is available in the Ubuntu repositories :
sudo apt-get install dirdiff
Now launch the tool from a terminal to compare or copy files and folders :
dirdiff
dirdiff
is a GUI for diff
and can handle up to 5 trees. It displays a main window with a list of files which are different between the trees, with colored squares to indicate the relative ages of the versions. A menu allows you to display the differences between any two of the versions in another window. Another menu allows you to copy files and folders from one tree to another.
Summary : Most relevant of all is the quality of the USB disk and its writing speed capabilities !