Just FYI, I used Peter's walkthrough to get my flirc working with my remote and it was working perfectly. Thank you Peter! Today I turned on my Ouya and it had an update to install (fw version 1.0.459_r1). After the update my remote stopped working. The arrow keys worked fine but the O and A buttons wouldn't work anymore. I couldn't select anything. I had to repeat step 3 of Peter's walkthrough and then unplug the FLIRC and then plug it back in. After that the remote is working properly again. I had noticed that the Vendor_20a0_Product_0001.kl file was no longer present under /system/usr/keylayout.
So in case yours updates and your remote stops working the above should help.