Following a recent driver change from Atmel we are aware of a problem with the AVRISP mkII working with Flowcode.
The error will be related to: avrdude: usbdev_open()
To fix the error follow the steps below.
1) Download the latest release of libusb-win32 from http://sourceforge.net/projects/libusb-win32/
2) Unpack the libusb zip and run the inf-wizard.exe in the bin folder AS ADMINISTRATOR
3) Select the avrisp mkII from the list that appears when you run inf-wizard then click next through the wizard.
4) When prompted select a place on your pc to save the .inf file that the wizard will create. (If you loose the file in the future you can simply repeat the task)
5) When prompted click OK to install the driver.
If required you can run the Atmel Studio 6.1 Jungo driver install again and revert to Atmel Studio drivers with the avrispmkII.
If you receive a message like this:
avrdude.exe: stk500v2_command(): command failed
avrdude.exe: stk500v2_program_enable(): bad AVRISPmkII connection status: Target not detected
Then it could simply be that you need to power the board using an external DC power supply.