Because you've got two long lengths of cable running to the battery you may have a large voltage drop across the cables when cranking the engine. The voltage may drop low enough on the permanent 12V line to your stereo so that it loses all the stored memory.
I'd recommend grounding your battery in the boot. Make sure it is a good earth (remove paint around bolt, use a star washer to bite into the metal, and find a meaty section of the chassis to bolt to). If that doesn't fix it run a new wire directly from the battery positive (via a fuse) to the stereo.
