This topic can be closed. I was unaware that flirc saved the config on the device, instead of the OS. Plugging it into my laptop and doing the configuration that way fixed it for me.
Just bought a Flirc, followed the instructions in the Download section to install the Debian .deb for flirc. When I run the GUI, however, I just get a 'Please connect flirc' error. Flirc is connected, as it shows up via dmesg and /var/log/messages.