Has anyone got the two to play nicely together? I did a fresh install and spent a few hours trying to get it to work with no luck. I did get a warning at the end of the install that states that there could be issues with the newer remotes so it sounds like it is a known item to be resolved. I wouldn't be surprised if I have it really screwed up now, so I'll probably take another whole 15 mintues to do another fresh install.

The following worked for me.
I backed up:
cp /etc/lirc/hardware.conf /etc/lirc/hardware.conf.orig

then nano /etc/lirc/hardware.conf

changed:
DEVICE="/dev/usb/hiddev0"

to:
DEVICE="/dev/lirc0"

saved then rebooted.

I'll have to try that after the fresh install this evening.

It worked! However, after editing and then rebooting it didn't work. I then ran lirc-reconfig.sh and then edited it again as instructed and for whatever reason it worked that time.