Why does deleted content reappear on my iPhone when I connect via USB?

I recently upgraded from a 3GS to a 4S, and I'm having an issue that's never been a problem before. I notice that music or video that I delete from my iPhone reappears when I connect to iTunes via USB. Nothing is moved over, either: the videos are just listed as if never removed.
I am deleting this videos by swiping across after viewing on phone. They disappear, so I am not overlooking anything on that front. Similarly, I don't sync video or music -- I have manual management checked in iTunes.
Any ideas what might be happening, and how I can fix it?

And almost 2 years later this is still happening - I delete TV Shows and Movies from my iPad 2 (iOS6) or iPhone (iOS6) and as soon as I connect the devices to my mac by USB they reappear (even though my setting is to manually manage everything). This then screws up syncing like this morning where I tried to add 2 new movies - as it was syncing I realised that the previous 2 had reappeared so I wouldn't have space to add them. I deleted them via iTunes and the sync appeared to be successful - until I turned on the iPad on the train to be greeted by a message saying that the 2 items couldn't be synced.

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Welcome to the Apple Support Communities!
If iTunes is not recognizing your iPhone on your Windows computer, please follow the troubleshooting steps in the attached article.
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