OS X keyboard weirdness

I’ve encountered some utterly confusing keyboard behavior with Renoise and my macbook pro running os x 10.8.4

If I enable function key behavior in OS x’s system preferences, the command key no longer works within renoise. Any shortcut that uses command (cmd+o, cmd+ 1, etc etc) no longer functions. Keyboard shortcuts that use alt/option still work fine.

If I enable “Use right side modifiers as Modifiers Only” then the cmd+ shortcuts start working. However, I can no longer use the keyboard for note entry!

Everything goes back to normal if I turn off “Use F1-F12 as standard function keys” in OS X’s system preferences.

It isn’t too difficult to get used to using fn+F key to access the commands, but it took me a couple of days to figure out what the heck was going wrong, so I figured I’d log it here.

This has been reported before (and Renoise is not the only application having problems with that), i know Taktik gave an answer on one of these posts, but i can’t find it anywhere.
I thought the bottomline was to not use that function with applications that require use of these keys.