Window key suddenly stopped working as Cmd key

I bought a CM Storm Quick Fire mechanical keyboard and it has worked wonderfully with my Mac after I worked out how get my iMac to work with a British-PC keyboard. Recently, the Window key which has been acting as the Command key, completely fine, suddenly stopped doing this action. It's both Window keys and the key configurations have not change, so I don't know why this had happened.

I swapped my Alt key to work as the command but that then lead to the Option action to no longer work with the Window key. Has anyone else had this issue and managed to fix it?