its good that uve read the dependencys for the newer firmwares Tongue

for firmware 1.2.5++ you need cmigner 3.3.2. not 3.3.1

yes, I have 3.3.2 cgminer installed...

tell us more what kind jtag did you use and what kind firmware file you use .hex or bin?

upgraded cgminer to 3.4.0 - no any changes.
I have used AVR Dragon, compiled the firmware with Atmel Studio

you make sure program right mcu for your Jal.