Thanks for the replies.
Where are you copying to?
I'm actually copying to another Fedora machine, so I don't think this is the problem.
Thanks for the tip about the arguments, I'll give it a shot without the -rpg to see if it helps any. As for the -q, I'm only using that to cut down on some of the text that shows up. Running it from terminal via python produces the same text over and over again ('file not found' when the folder is empty for instance), so I wanted to keep that to a minimum. Even before I did that though, I didn't see any errors. It just keeps copying all the files over each time.
Iainr, does that setup you're using do incremental backups, or is that doing everything each time it runs? I thought the -u argument was needed for incremental.
Edit: Couple things to add. First, it seems it's not copying every file over each time. It is however copying the same group of files over each time. I don't know how it's choosing the files it's moving, but there are still quite a few that are copied each time. It doesn't matter if I use the -u or not either.. it always seems to only do certain files, even though none of them have been changed.
Second, it appears I'm not the only one having the problem. A quick check at http://samba.anu.edu.au/rsync/
shows that this is in the FAQ, and that people are still experiencing this issue, and have been for a long time. Unfortunately, it seems that nobody have found a way to get it to copy only modified files yet.