HD and SD shows not syncing properly

I downloaded a couple of the free HD episodes when they were first made available and bought a couple of episodes of Law & Order:CI. Initially, the SD episodes synced to my iPod and the HD to my AppleTV with no problems. Just to clarify, the SD episode didn't even show up in the episode list on my AppleTV and I never got any warnings about the HD episode not playing on my iPod when I synced. Also, if I watched one, HD or SD, the other would also be marked as played.

Now, both versions show up on my AppleTV (and look the same BTW so you can't tell which is which) and I get warnings that the HD version won't play on my iPod when I sync. Additionally, the "marking as played" functionality isn't working anymore.

What's the deal? Is this a temporary issue? I have to say the way it was working initially was pretty slick and now it is just cumbersome and annoying.