I have a similar issue, my old flirc is on Firmware: v255.7.0 [0x020A07FF]. The GUI just says it's too new and won't update it.
On ubuntu, the flirc_util is still bundled with the GUI. So what I did was:
sudo chmod +x /usr/bin/flirc_util
then you can run things like
/usr/bin/flirc_util version
That should tell you if it's working. Now to update it here is what I just had to do (what a pain in the balls).
on Ubuntu:
sudo apt-get remove flirc
wget http://apt.flirc.tv/arch/x86_64/backup/flirc_1.2.6-1ubuntu1_amd64.deb
sudo dpkg -i flirc_1.2.6-1ubuntu1_amd64.deb
Flirc
Then it updated the firmware to 2.6.0. Half way there!
sudo apt-get remove flirc
(gets rid of 1.2.6 version)
sudo apt-get install flirc
(re-installs 3.1.0)
Flirc
(now it prompts you to upgrade the firmware)
I don't really enjoy having to scrape through archive.org to find the old repository to get an older version, kind of lame.