Input Method Keys not Firing Event
Maybe it's not recognized as a JIS keyboard. See http://m10lmac.blogspot.com/2009/12/fixing-keyboard-type-problems.html:


  Sometimes a machine will forget which type keyboard is attached, with the result that certain keys get transposed from what the user expects. The fix for this is run the Keyboard Setup Assistant again. Sometimes there is a button for "Change Keyboard Type" visible in System Preferences/Keyboard. If not, you can try trashing the file
  
  /Library/Preferences/com.apple.keyboardtype.plist 
  
  Another possibility may be to open Terminal and type:
  
  sudo open /System/Library/CoreServices/KeyboardSetupAssistant.app/Contents/MacOS/KeyboardSetupAssistant
  
  Sometimes, when JIS is involved on a laptop, one may have to follow the procedures in the PMU Resetting instructions. 


If nothing else works, you can use KeyRemap4MacBook to map other keys to かな and 英数 keys:

&lt;autogen&gt;__KeyToKey__ KeyCode::F1, KeyCode::JIS_KANA&lt;/autogen&gt;
&lt;autogen&gt;__KeyToKey__ KeyCode::F2, KeyCode::JIS_EISUU&lt;/autogen&gt;