I ran into an issue today where issuing back to back avrdude commands will fail when using dragon_isp on Ubuntu 10.10
Summary is some applications like the Arduino IDE
issue back to back avrdude commands (1 for fuses and 1 to program the bootloader) and the second command fails
because avrdude resets the device and the device must
then enumerate with the OS again which can take some time.
Until enumeration is complete the device no longer exists
so the second command fails.
I don't believe that this will be limited to the dragon on Ubuntu.
See the Savannah bug filing for more details: