Looks like Farrington is about to go out of business. I think it's quite clear from the initial post as well as from this on the CX website that this fee refers only to non-CX ticket stock:
I think problem was with the statement given to OP (and travel agents) by CX. The statement was not very clear as it did not specify that the fees apply ONLY for non-CX ticket etc. The statement on the website is clear.