It is very difficult to get FedEx to do anything about the account numbers that you suspect are being used for fraudulent purposes either online or by telephone.
You could always try their online form
http://www.fedex.com/gb/contact/writefedex.html and just say that you have received a fake check despatched from one of their account holders and what can you do about it ?. Keep it short and simple because the person who reads simply won't understand if you go into too much detail, just wait for a reply.
If you are in the USA your Postal Inspector will be interested even though it's a courier firm that you have information about.