some time ago I had this remote working under Pluto, but :
if I remember right, I had to do few things :
- disable kernel module that makes RW acting like mouse
- add Ati Remote Wonder as lirc remote
- stock configuration file didn't work for me, so I recorded new one and I guess contributed back into Pluto database
- I also remember that lirc was not working and I ran out of ideas, but then after few reboots it started to work - no clue why...
So maybe you should try to get it working with lirc manually, record buttons and see where the problem is...