My guess at this stage is that your remote is operating as an extra USB keyboard. It's possible there are settings in the BIOS for using a USB keyboard that you could play with, maybe in conjunction with 'xev' to see if the X server is capturing any events from the remote. Another poster had the problem that his remote was interfering with the built-in keyboard on his notebook.
I never used a USB keyboard, so I'm not quite sure what to expect.
As a last resort you can recompile lirc with the debug option enabled, and even add extra debugging code to the dev/input driver. There is some documentation about the USB input system in directory Documentation/input of the kernel source code (especially input.txt), but I never got my head around this stuff.