I'm not really expecting a solution to this, just ranting/reporting an oddity. It confirms my general distrust/hatred of USB in general! :-)
I have a little Acer Aspire netbook that I use (as I am now) when away from home, it runs xubuntu 11.10 (though I'm fairly certain I saw the same problem with previous versions of xubuntu).
I use a Genius/Kye Traveller 350 mouse with it rather than the horrible touchpad. This works beautifully as it's actually a trackball rather than a mouse and has a scrollwheel and a fourth button that I have programmed as a double click of button one - bliss! :-)
However after a random amount of time the Genius mouse stops working, since this is quite a long time (like hours rather than minutes) it doesn't often worry me too much as I don't spend hours on my laptop. Tonight though I decided to have a play and see if I could work out why it stops working (as the netbook had been left turned on and the mouse had, as usual, stopped working).
I have the mouse plugged into the left hand side of the netbook where there are two USB ports as I usually use it left handed (even though I'm actually right handed). Since it had died just now I unplugged it and plugged it back in a couple of times, nothing, dmesg/syslog shows nothing, it's as if the mouse doesn't exist. If I reboot though it will work with no problem.
Then I tried plugging it into the USB port on the RHS of the netbbok, and it works! It's still working. I can plug/unplug it repeatedly and it works every time. If I plug it in to the LHS ports there's still nothing happening though. Other devices (e.g. memory sticks) plugged into the LHS USB ports work perfectly though. It's just the mouse that won't work in the LHS ports (until I reboot!).
Wierd! I think USB is a creation of arcane beings.