Command and Option keys on Windows keyboard

Do you have the Logitech Control Center (LCC) software installed?

if so uninstall it and see what happens.

(I had a few issues when I had it installed with crashing and strange things happening to my keyboard (I only had a Logitech Mouse) which at the time all the knowledge on the interwebs told me was down to LCC being a pile of horse puckey.)

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:

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