Some people are having a problem flashing the contiki AT90USB1287 .elf file with AVR Studio/JTAGICE mkII. Google found this from June 2008
which says Studio erroneously flashes too much data to progmem, basically everything in the .elf file including debugging information, and that this might be fixed in a new version.
All is working for me with AVR Studio 4.14, but I note that the .elf flash is indeed excessive, writing an extra copy of the bootloader as well as debugging information.
I am wondering if AVR Studio 4.15 fixed the problem and possibly introduced a bug?