It's the protocol, you need to record every key twice. Once I get back to development on this, it will be fixed.
No inter-key delay in the second version of Flirc.
Don't hit 'start' on the GUI. Essentially press the button in the GUI you desire to record. Press the remote button you want paired. Do the immediate action again. Every time you hit the same button on your remote, an alternating pattern is sent out. If you press another button before the same button again, some remotes just sound out the first button again. So it's critical you manually record each button twice and in a row.