I tried a couple of remote settings, only setting my Universal remote to work was either Samsung or Panasonic, although with limited functionality. When using either Panasonic or Samsung device some of the buttons are disabled by default for some reason. Normally this would not be an issue, I would just put my Universal remote into learning mode and it would work. But I don't have a Samsung or Panasonic remote to do that. I tried a old XBOX DVD remote, IIRC it should work out of the box with a MCE IR dongle. Nothing worked on that remote.
I did notice when programming the Flirc, I received messages that the button already exits. A second try work however.
For Linux I should have guessed needed root to program the Flirc. Might not be a bad idea to test if the OS is Linux and if the User is root, might make it a bit more friendly.