[JasonPell]

I managed to resolve this myself. LIRC.Stop was indeed doing what it was supposed to. Unfortunately XOrg was registering my remote as a keyboard / mouse as well, so regardless of the LIRC support being turned off, Xorg was still generating equivalent keyboard events.

Thanks to this post:

http://ubuntuforums.org/showthread.php?t=1683015

I now have a well behaved feature which does not trigger the IR

I added the following to /usr/share/X11/xorg.conf.d/90-mce_usb.conf and restarted X Windows. I then added the LIRC.Stop and LIRC.Start to my
browser python script and all is well.

Section "InputClass"
Identifier "Ignore MCE_USB as Keyboard input"
MatchProduct "Media Center Ed. eHome Infrared Remote Transceiver (0609:0334)"
MatchIsKeyboard "true"
Option "Ignore" "true"
EndSection

Section "InputClass"
Identifier "Ignore Second MCE_USB as Keyboard input"
MatchProduct "MCE IR Keyboard/Mouse (mceusb)"
MatchIsKeyboard "true"
Option "Ignore" "true"
EndSection