Got past the problem with trying to uplaod the 2.6 firmware. I just had to exit and restart the FLIRC gui a couple of time. The first time it detects the bootloader and upload the 3.5 firmware. IIf I immediately try to upload the 2.6 firmware, it crashes. To get it to work, after it uloaded the 3.5 firmware, you have to exit FLIRCGUI. On the next restart, it correctly detects the 3.5 firmward (not he bootloader) then you can successfuly upload the 2.6 firmware.