I am experiencing this issue in Intrepid.
I have an external hard drive (WD) that is hooked up by a USB cable.  Small 
files transfer fine, and the HD works flawlessly in vista.  However, using 
Ubuntu, During large file transfers, the system randomly locks up.
At the start of the transfer the transfer looks smooth (i.e. the ##mB 
transfered increments steadily), then it starts jumping up instead of steadily 
increasing (i.e. it jumps from 90mB to 120 then to 150, etc..) and then it 
stops at a certain point.  Usually this point is over 500MB, but other than 
that it seems to be random (even when transfering the same file, it stops at 
different points).  When I try to close the transfer or cancel it, the window 
does not respond.  Then after a few seconds the desktop background and the 
top/bottom ubuntu panels become frozen.  I can restart GDM, but doesn't solve 
the problem - GDM doesn't load properly - only loads background I think.  I try 
to shutdown, and it wouldn't do it... GDM closes but then it gives me some text 
(something about SDC), and sits there, so I have to do a forced reboot.  The 
message that it gives me wasn't very helpful anyway, it made little sense.  If 
someone wants to diagnose the issue properly, please let me know and I'll try 
it again and tell you the message.  Also, ubuntu won't start up again unless I 
shut off the external hard drive and turn it on again.

A few times I was able to close the transfer (can't remember how, but I 
remember it involved waiting for like 5 minutes).  Then I did "lsusb" and the 
hard drive doesn't show up. I tried shutting off the HD, turning it on, and it 
won't show up, and I couldn't mount it in ANY WAY  So I ended up having to 
reboot the system and the HD before they can work again.
Here are my specs:
Thinkpad Notebook T61, 2.0Ghz, 2GB 667Mhz DDR ram, X3100 video card, usb 2.0, 
80GB SATA internal drive
Ubuntu: Intrepid Ibex (did fresh Intrepid install, and applied ONLY critical 
updates --> still problem)
uname -a:
Linux ls1 2.6.27-9-generic #1 SMP Thu Nov 20 21:57:00 UTC 2008 i686 GNU/Linux

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System eventually freezes during large data transfer from samba share
https://bugs.launchpad.net/bugs/104256
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