I found someone with a similar problem here.
It seems the Kinesis keyboard has a multimedia setting.
Finally, I found the answer on the Kinesis FAQ. My F3 and F4 keys were behaving like multimedia keys (see manual to configure these). This feature can be disabled by holding = and pressing P for PC (you can also use W for Windows and M for Mac).
So try =+P and see if it's resolved. (or =+W or =+M)
From the FAQ:
9. Function keys not working on USB Advantage Keyboard
It's possible the "Multi Media" features of the keyboard have been enabled, which changes some of the function keys.
To check, open up some kind of text editor and press and hold the equals key and tap the letter "s". You should see some text on the screen. If you see any of the function keys listed inside the brackets [F3 F4 etc. ] then you know the Multi Media features are active.
Normally, this is turned on by holding down the equals key and tapping the letter "n."
To disable the Multi Media feature, enter the Instant Configuration you're currently in.
So for example, if your keyboard is in Windows Mode, select Windows mode by holding down the equals key and tapping "w" (=w). (=m for mac mode and =p for PC mode)
This will clear the settings and your function keys should behave as expected.