I too have had a problem which sounds similar whereby my USB device
would spin down and wait 10 or so seconds before spinning back on every
segment of a large file copy and after more research came across a
thread for bug #88746 (https://bugs.launchpad.net/ubuntu/+source/linux-
source-2.6.20/+bug/88746) which after reading this thread may apply to
some of the scenarios descibed above.
This thread has two fixes both of which worked for me as follows
1. This one can be done without the need to rebuild a kernel (I would
try this first and if it works for you either build a udev rule so that
it is always included at boot or look at the second option).
modprobe -r ehci_hcd
echo -n -1 > /sys/module/usbcore/parameters/autosuspend
modprobe ehci_hcd
2. The second one requires applying a patch and rebuilding the kernel, I
also recreated my initrd file as the ehci_hcd driver is also preloaded
in these on my system
http://www.kernel.org/pub/linux/kernel/people/gregkh/usb/2.6/2.6.24
/usb-ehci-add-a-short-delay-to-the-bus_suspend-routine.patch
--
USB mass storage stops working after a while
https://bugs.launchpad.net/bugs/61235
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