Alfie,
Are you synching playlists or smartlists? If smartlists, do any of your smartlists have rules that are executed dynamically (i.e. random, limitations by size, time or duration)? If so, the contents of these smartlists will be changing and unless all of your files in MC are on iPod, this could explain your results.
Do you have 'Delete unselected from HH' checked?
If there is a file that keeps being resent, please email it to me. There may be a reason why MC is not catching it as a 'match' by its name, artist, album, genre, track number key which also could explain what you are seeing.
Steve (steve @ jriver.com)
PS also, what do you mean by having done a 'Partial sync' and then the statement that nothing is changed? Did you stop a sync in the middle? If so, if you try to sync all the files again, it may be accurately reporting to you that at the end of the sync, you will be out of space.