If you see an Atmel device when running lsusb (03eb:2ff?) that means
the board is connected in DFU mode. The most likely problem is that
the makefile is not set to MCU=atmega32u2 or that you have not enabled
permissions with a .rules file:
http://code.google.com/p/micropendous/wiki/SettingUpUbuntu904Linux
Try running dfu-programmer directly with sudo and see what happens:
sudo dfu-programmer atmega32u2 erase
sudo dfu-programmer atmega32u2 flash YourFirmwareName.hex
sudo dfu-programmer atmega32u2 reset
If the above work then you can either run sudo make dfu each time
you program your device or you can add your device to a .rules file:
http://code.google.com/p/micropendous/wiki/SettingUpUbuntu904Linux
One other possibility is that the picture in the instructions is for
an AT90USB128-based board on which the buttons are in the reverse
order to the Micropendous-32U2. Make sure you press HWB and RESET,
then release HWB, then RESET.
If you are still having problems please post the relevant lsusb and
dmesg text.