My own fault actually- was running V1.3.6 of the GUI which wasn't playing nice with the v3.7 on the FLIRC. Updated to V1.3.7 of the gui and all now working as it should. I musn't have dropped the Flirc 1.3.7 GUI into the Applications folder the last time I ran it to update the firmware so was still running V1.3.6...