When I check to see how much memory is in use on the phone (not the memory card) it reports 4177kb, but the breakdown that follows doesn't come anywhere near this value, are there hidden directories and the like in the phone memory? What do these contain?

Yes, could be. To understand better phone memory, read this: http://www.allaboutsymbian.com/features/item/Keeping_It_Clean.php

Thanks but that article refers more to RAM than the phones internal storage memory.