No, it's not Ubuntu specific and Canonical didn't cause it.

Right now I'm copying between two SATA drives, connected to my PC via
eSATA.  So far a lousy 600MB has been copied and I'm already down to
5MB/s and falling.

Here is what I know about the problem:

It affects ALL hardware.

It affects ALL file copying connections to varying degrees: USB,
network, SATA/eSATA.

In some instances, it also affects multitasking, all but locking the
computer up despite little to no CPU use in System Monitor.

There are no error logs, messages or anything else that occur when the
problem is happening.

In my experience, if you test for the problem and nothing seems to be
wrong, then that's because you aren't copying enough data, you don't
know how fast your hardware should be copying files, or you are lucky
enough to only be subtly affected that time.  Try copying more multi-
gigabytes of data, several times and see if you can't get wildly
different durations for the same data size.  As I state above, all
hardware I have tested is affected to varying degrees, some hardware
shows minor performance degradation over time, some hardware is all but
useless for file copying.

If you ask me, it's either the scheduler (GUI lockups with no CPU usage
makes me think this) or whatever performs the actual file copy process.
It's definitely not a USB problem because it affects network copying
too.

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