I did a bunch of tests. First of all, I'm attaching the output of:

cat /proc/version_signature
dmesg
sudo lspci -vvnn
sudo lsusb -vv

I used Ubuntu Jaunty kernel "2.6.28-9-generic", except for the log of
"lsusb", which was acquired when the system was running under
2.6.29-rc7, vanilla, from kernel.org.


The system is the latest Kubuntu Jaunty alpha with updates as of 10 March 2009; 
architecture: AMD64.
I did the tests running KDE 4.2.1-0ubuntu5 and used the automatic "pop-up" 
feature to mount a 16-GiB USB pendrive specified for a minimum throughput of 
approx. 14 MiB/sec.


These are my observations:

Copying large files (i.e. approx. 8 GiB) from high-performance harddisk to the 
USB drive using 
_Microsoft Windows XP SP2_, the above-all average transfer speed is 13...14 
MiB/sec. This is always reproducible.

Using my Ubuntu system: 
When _copying large files using KDE_, after the first 3GiB or so, the transfer 
rate drops from the initial 14 MiB/sec to an average of about 5.5 MiB/sec. The 
indicated speed on the progress window fluctuates between a few kiB/sec and 
full speed.

Using the _command line_ and timing the following commands using a
shellscript yields /slightly higher/ average transfer speeds, approx. 7
MiB/sec.

Ubuntu kernel 2.6.28-9-generic and a custom 2.6.29-rc7: No difference.


Conclusion: Using Ubuntu, the transfer speed is always less than half the speed 
than under MS Windows XP.

I did at least 20 tests with different file sizes, file systems on the
pendrive (VFAT, EXT2, fuse NTFS3G NTFS)

-- 
file transfers on USB disk are very slow
https://bugs.launchpad.net/bugs/197762
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