There are two ways to get the application version and a firmware version using the commandline version. The command version, will give us both the application and the firmware, or simply running the commandline by itself will by default print out both the versions, and the commands available.
bash $ flirc_util version flirc_util version v2.3.0 [v2.3.0-2-g3bdde39+] Firmware: v4.0.16 [0x4E3178B5]
The version of the applicaiton will always be in sync with the GUI version. They will never not be the same, and if they are... call the police.