Yeah, it's a good day for me..
I've finally discovered why my mkII and my dragon had so many connection problem and timeout issues while I was debugging my application.
I use Ubuntu on my notebook and I use avrstudio in Windows xp virtualized in vmware.
The problem isn't vmware, the problem is that my processor (core 2 duo) varies his clock frequency in base of load.
Every time it happens, I have a problem in communication with mkII or dragon.
The solution is to force the processor to work at the same frequency. Is not important what frequency, fast, slow, medium, but the frequency must never change.
I hope this will helpful to someone.