It appears that there is an issue where iPlayer does not do the delete of downloaded programs properly if you delete them immediately after you have watched them.
If you are in the habit of doing this I suggest you look in the iPlayer repository (usually found within My Videos but if you untick Allow BBC iPlayer Desktop to manage where programs are stored in the prefernces it will show you where it can be found).
Anyone else found anything left behind? (I found 3.8GB!)