I was able to reproduce this bug with the latest updates.

I am copying files from an external USB disk using the FAT32 filesystem
to an internal ATA disk with the EXT4 filesystem (SATA disk on PATA
controller).

I will run fsck on both partitions to make sure there are no error that
show up. If there are I will attempt to fix them.

The only thing special about the output of my cp -vr (as requested) was
that the copy did not happen in alphabetical order, It started at a
folder which begins with the letter F and then skipped to k then J then
S, copying file sporadically. I expected it would copy all the folders
in alphabetical order.

In nautilus I noticed that an 7.8GB copy reported at:
3:01pm - 100.7MB of 7.8GB -aprox 4 hours left (542 KB/sec)
3:29pm - 342.5MB of 7.8GB -aprox 12 hours left (176.5 KB/sec)
3:49pm - 501.6MB of 7.8GB -aprox 13 hours left (161.0 KB/sec)
4:05pm - 632.3MB of 7.8GB -aprox 13 hours left (156.9 KB/sec)
4:35pm - 846.7MB of 7.8GB -aprox 13 hours left (151.5 KB/sec)
5:14pm - 1.2GB of 7.8GB -aprox 13 hours left (146.9 KB/sec)

I noticed that although I am not using my computer for anything else,
transfer go slower over time. In my experience, it just stops somewhere
in the middle and never finishes. I expected that the speed would be
consistent if I did not slow down my computer with other processes.

-- 
[Lucid] Copying multiple files causes "Input/output error" and "No such file or 
directory" errors
https://bugs.launchpad.net/bugs/551110
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