Since some remotes send alternating codes and there are multiple questions/postings about having to record the same key twice, why not record two key presses when going through the setup? The second press could confirm the original code, or determine if the remote alternates codes between presses. If users don't want to go through this process, you could also just make this an option in the Advanced menu "My remote uses multiple codes per button".
1) Press a button on the gui or use the flirc_util record command
2) Prompt user to press a button on the remote
3) User presses button on the remote
4) Acknowledge the code was received and prompt the user to press the key again
5) User presses same button again
6) Acknowledge the second press. If the codes are the same each time, record the first code. If they are different, record both. You could even prompt the user to press the button again, to recognize that the third press matches the first.
This would eliminate the headache for MCE style remotes.