or is this problem unique to my situation?
No it is not unique, I'd say it's common on linux.
I've been experience the same situation twice,
os : ubuntu 10.10
1. I just restart computer,(don't know why it remember the status of ports , if you plug/unplug
usb , computer still remember the status, probably some variables keep info till system is running).
2. Than start IDE, after restart of machine.
3. Open simple sketch, like " blink" from examples.
4 Connect usb plug in from the board (should be disconnected during restarting).
5. Press upload a sketch when it negogiates usb settings, tx and rx leds blinking at that time.
As they say there is a solution to refill 8u2,
for me? I will stay with a bugs, at least I know them,
instead to encounter some new bugs that I was not aware off.