Thank you for your answer.

I found an other solution which fix my problem. I just plug the board on a windows 7 pc with arduino-0022, instead of ubuntu 10.10. 64bits with arduino-0021.
There is no freezes anymore and I can upload sketches.

Do you think that the problem comes from arduino's software's version or from linux ?

Do you know where I can find the arduino-0022 for linux 64bits ? Maybe it will fix the problem if it comes back.

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 :'()