ITunes refuses to copy TV Shows based on episode numbers...!

I have a lot of TV content in iTunes, some bought from the iTunes store, some I have ripped and encoded myself. Everything is tagged thoroughly and correctly with episode IDs, episode numbers, watched/unwatched flags, series and season info, even episode titles. The works, basically. Everything appears in the correct order and works perfectly from iTunes itself.
However, when it comes to syncing with my iPhone, it's a totally different story. I have iTunes set to copy over the first least recent episode of various shows, and this used to work fine. Then it started to get things a little off, so I may have watched episode 1 and 2, but it would sync episode 4 instead of 3. Then it got worse, much worse, to the point I am now where it's as if I have some hidden 'copy any random thing you like' option checked.
To try and remedy this I deleted my iTunes library XML and uninstalled iTunes. I then re-installed, and set everything up again (not a fun process!). Then I let it sync my iPhone and if anything the selection of episodes it copied over was even more crazy than before.
I don't know what else to try here. iTunes itself displays everything perfectly and in the correct order, but I really liked the ability to keep things in sync between iTunes, my iPhone, and my Apple TV. I can use playlists and manually choose which video to sync, but I shouldn't have to.
Any ideas how to fix this? Thanks.

does a a Exclamation mark appear beside the name of the song?

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