I read it, but didn't really understand it. This is not what I call a reproduction scenario, as you haven't explained anything, nor detailed any of the settings in ir3.conf or irmode which will interact in some way. Nor have you stated explicity which version you are using (I presume 1.21 or 1.22).
Take it back to first principles and assume little knowledge on the part of the reader (and you wouldn't be far wrong). I don't really want to read the whole thread to pick up all the significant facts.
What is "f1"?
3,4,13 generates "1 2 OK" not "1 3 OK" so would attempt to select channel 12, not 13 as described.
It would be useful to know what you are doing and why i.e. what keys you are pressing and for how long, what you expect to happen, what does happen etc.
And forget describing anything that happens with anything apart from the standard RM-F04 remote (not the RM-F104 as you called it), as I don't have anything but.
I see some sort of linked list in the C code, pertaining to something called foreign codes, but I have no idea what that actually means. The config item line seems to have to start with a 0x. The linked list code appears to be deficient though. How should this be tested?
And to answer an old question, the size of the ir3.map file is limited to 4096 bytes!