I finally succeeded with some combination of unplugging the usb and hitting the reset and trying to upload. Really frustrating experience. I've learned to never do that again.
I have the same problem as JimH, but I didn't finally succeeded to upload my sketch.
The reply #34 on the topic "Problems with 0021 on Ubuntu 10.04 Lucid Lynx" say :
Don't try this unless you are prepared to risk bricking your board completely!
So, I am not very enthusiastic to reflash the firmware with dfu.
How can I upload a sketch on my arduino 2560 ?
(I had to put a delay() before :'()