I was testing the demo version of remote buddy ajax remote (iPhone) and found the same problem. XBMC doesn´t work while other software does.

I tryed wii mote with the same result, everything worked but XBMC.. until I found a setup option in system "allow other software to control XBMC" and voila!! everything works flawlessly.

Hope this helps ;-) 
(PD: this is my first post, i´ve just register to contribute, i don´t know if you have allready found that option)