First, function keys are not necessarily “normal” when pressed; by default they also require “fn” to be pressed, otherwise they perform a system function (Dashboard, sound volume, etc.). And since you can turn off a lot of these features in System Preferences, I can imagine that these keys might be set to do nothing.
It is also possible for Mac applications to install system-wide hot keys, theoretically overriding even single key presses. At the very least you need to know what apps are currently running to debug this.
It is also possible to install your own keyboard overrides, through System Preferences. Need to check those.
I’m probably missing some other things. The Mac is extremely flexible when it comes to the keyboard.