I'm just working through the keymaps for my Flirc/Ouya/Harmony and came across your post.
Care to share your .kl file? I'm not sure I understand what you have changed in the files above to get the fix for enter and escape working on the remote.
Are you mapping the Ouya controller O and A buttons to act exclusively as enter and escape respectively on the Ouya itself? Does this affect the usability at all? I've noticed that I HAVE to use the O and A buttons on the controller some times so wouldn't removing the map for those also remove their ability to behave as intended and render the controller useless?
I have my Harmony setup well for navigating plex as plex interprets enter and escape correctly. It's just when I get back into the main menu's that I have to use the controller to navigate around/back into plex.
Thanks in advance.