@kazz there are all sorts of things you can argue for a code 46 PCN, but at the moment you're on the wrong track. The code is not incorrect because red routes have a blanket stopping prohibition, there are certain exemptions but if the exemption does not apply (for example if you stop on a loading exemption to the stopping prohibition but you're not loading) then you're in breach of the red route stopping prohibition.
Have you got the CCTV footage? If not, call TFL first thing on 0343 222 3333 and ask for the video, they will send you a DVD in the post (ask them to put the penalty on hold while you wait for the video).
Please post up exactly what you sent, and TFL's reply.
Also a very basic question: where you actually loading? Waiting to load and loading is not the same thing, so it would be helpful to have a full account of the facts, from the moment you stopped to the moment you drove off again.
Lastly please give us the PCN number and number plate, or better still re-post the PCN with just your name and address redacted.