How to get Mountain Lion to recognise modifier keys from external Windows keyboard
Did you select the keyboard from the menu at the top? (Edit: it is not shown if there is only one keyboard.)



If you have installed keyboard or HID drivers, try removing them.

You could also try deleting ~/Library/Preferences/ByHost/.GlobalPreferences.*.plist.

Another way to change the modifier keys is to use KeyRemap4MacBook:

&lt;?xml version="1.0"?&gt;
&lt;root&gt;
  &lt;!-- &lt;devicevendordef&gt;
    &lt;vendorname&gt;KINESIS&lt;/vendorname&gt;
    &lt;vendorid&gt;0x05f3&lt;/vendorid&gt;
  &lt;/devicevendordef&gt;
  &lt;deviceproductdef&gt;
    &lt;productname&gt;ADVANTAGE&lt;/productname&gt;
    &lt;productid&gt;0x0007&lt;/productid&gt;
  &lt;/deviceproductdef&gt; --&gt;
  &lt;item&gt;
    &lt;name&gt;swap_command_and_control&lt;/name&gt;
    &lt;identifier&gt;swap_command_and_control&lt;/identifier&gt;
    &lt;!-- &lt;device_only&gt;DeviceVendor::KINESIS, DeviceProduct::ADVANTAGE&lt;/device_only&gt; --&gt;
    &lt;autogen&gt;__KeyToKey__ KeyCode::COMMAND_L, KeyCode::CONTROL_L&lt;/autogen&gt;
    &lt;autogen&gt;__KeyToKey__ KeyCode::COMMAND_R, KeyCode::CONTROL_L&lt;/autogen&gt;
    &lt;autogen&gt;__KeyToKey__ KeyCode::CONTROL_L, KeyCode::COMMAND_L&lt;/autogen&gt;
  &lt;/item&gt;
&lt;/root&gt;