I figured out, important for Logitech Harmony users, that programming FLIRC directly from the Harmony ends up in a total mess.
I used a faked, old, remote and just mapped all OUYA controller buttons to the keyboard layout from Peter. Afterwards added this remote as device in the Logitech Software and mapped the buttons accordingly.
Now works as expected.
I you add a device to the Harmony via the Logitech software and then try to program FLIRC directly from the Harmony you have to expect a strange behaviour and you may have to edit settings (so it reacts slower or faster, done in the Logitech Software) or just use any old Remote to program FLIRC first and then the Harmony.