I think I'm having a related issue although I'm using a Yamaha RAV370 universal remote.
I recently upgraded Flirc to 1.3.4 (fw 3.5) and suddenly my keymappings stopped working. I reloaded my config to no avail so I decided to start re-programming it.
This remote sends alternating key sequences so I have to record two key presses per key assignment. I'm finding that in some cases Flirc is reading the second key assignment as a previously assigned key. as an example, let's say I assign the up arrow , then I assign the left arrow, the second key assignment for the left arrow will sometimes become the up arrow. It will pop up a "Button already exists!" dialog box.
I've followed some of the troubleshooting tips from this page: https://flirc.zendesk.com/hc/en-us/articles/204074695-Flirc-isn-t-sending-the-correct-function-to-my-device
are there any additional diagnostics / troubleshooting available?
all of this worked properly with firmware 3.3, is there any way to downgrade the firmware for a quick fix?
I'm using Flirc on a mac running OS X 10.7.5. I didn't see any command line utilities for the mac.