Just got a chance to look at this again. I still seem to be having a problem. I have my joystick.harmony.xml file in the userdata/keymaps folder which I have edited with Up=22, Down=23, Left=24, Right=26 in the global section of the xml file. All other settings are left as they originally were in the joystick.harmony.xml located inside the XBMC.app (except for the other items which previously had 22,23,24,26 assigned to them. I added a 1 to the end of each of these to avoid conflicts). I verified these codes by running the custom XBMCHelper in --multi --verbose mode, where I see the following when pressing up, down, left, right - in that order.
mini:~ dan$ /Applications/XBMC.app/Contents/Resources/XBMC/tools/osx/XBMCHelper --multi --verbose
2009-12-14 21:43:16.244 XBMCHelper[43125:903] XBMCHelper 0.6 starting up...
2009-12-14 21:43:16.274 XBMCHelper[43125:903] [DEBUG] Driver has started successfully.
2009-12-14 21:43:16.275 XBMCHelper[43125:903] [ERROR] Driver has not found any remotes it could use. Will use remotes as they become available.
2009-12-14 21:43:16.276 XBMCHelper[43125:903] XBMCClientWrapperImpl started in multiremote mode sending to address localhost, port 9777
2009-12-14 21:43:29.807 XBMCHelper[43125:903] Change of remote ID from -1 to 200
2009-12-14 21:43:29.808 XBMCHelper[43125:903] Received button 'Minus' press event
2009-12-14 21:43:29.810 XBMCHelper[43125:903] XBMCClientWrapperImpl:
endButton sending button 22 down:2 up:0
2009-12-14 21:43:29.927 XBMCHelper[43125:903] Received button 'Minus' release event
2009-12-14 21:43:29.928 XBMCHelper[43125:903] XBMCClientWrapperImpl:
endButton sending button 22 down:0 up:4
2009-12-14 21:44:11.862 XBMCHelper[43125:903] Received button 'Left' press event
2009-12-14 21:44:11.863 XBMCHelper[43125:903] XBMCClientWrapperImpl:
endButton sending button 23 down:2 up:0
2009-12-14 21:44:11.863 XBMCHelper[43125:903] Received button 'Left' release event
2009-12-14 21:44:11.864 XBMCHelper[43125:903] XBMCClientWrapperImpl:
endButton sending button 23 down:0 up:4
2009-12-14 21:44:13.502 XBMCHelper[43125:903] Received button 'Right' press event
2009-12-14 21:44:13.503 XBMCHelper[43125:903] XBMCClientWrapperImpl:
endButton sending button 24 down:2 up:0
2009-12-14 21:44:13.504 XBMCHelper[43125:903] Received button 'Right' release event
2009-12-14 21:44:13.504 XBMCHelper[43125:903] XBMCClientWrapperImpl:
endButton sending button 24 down:0 up:4
2009-12-14 21:44:14.614 XBMCHelper[43125:903] Received button 'Menu' press event
2009-12-14 21:44:14.615 XBMCHelper[43125:903] [ERROR] No executable set. Nothing to launch
2009-12-14 21:44:14.615 XBMCHelper[43125:903] XBMCClientWrapperImpl:
endButton sending button 26 down:2 up:0
2009-12-14 21:44:14.616 XBMCHelper[43125:903] Received button 'Menu' release event
Then, I end XBMCHelper, go into XBMC and change the remote mode to Harmony (Multi), and set the option to keep XBMCHelper running in the background. I exited XBMC, then restarted it. Once back in, the up/down/left/right buttons do nothing. I exit XBMC, start up XBMCHelper again in --multi --verbose mode and this time it sees the up/down/left/right buttons as from remote 150 - the standard XBMC apple/harmony remote setup codes. To further weird this out, pressing my soft "weather" key on the harmony (which previously was identified as button 73 from XBMCHelper) suddenly switches to remote 205. From that point forward, the up/down/left/right keys identify as remote 200 again.
At one point when testing in XBMC and not having the up/down/left/right buttons work, I had hit the buttons several times in succession and noticed that FrontRow launched. The Right button would start and stop it. About a minute later it stopped operating FrontRow. I also noticed that one of the button apparently tried to start iTunes (I had the license agreement up after quitting XBMC - I do not use iTunes on my mini).
Now - while pulling my hair out, I got the idea that maybe my remote was sending different codes and going nuts. BUT - my RemoteBuddy configuration works flawlessly, so if my remote were sending random codes out, I would get some missed/incorrect commands even with RemoteBuddy.
Any light to shed on this? Something in this equation is just not right.