Multi-Season TV Shows Mixed Up

Windows 7 Professional, 64-bit; iTunes V: 11.0.4.4
It's been awhile since using iTunes, but I needed to purchase a bunch of new songs. After purchasing the roughly 12 songs, I plugged in my iPhone 5 to sync the updated playlist. There was still plenty of room on my phone for these few new songs. I left the computer to do it's work and when I returned, I noticed my phone said 30-some items could not be synced. I went to re-sync my phone and noted that some Battlestar Galactica episodes were adding. Since the episodes being added should have already been present on my phone (watching the whole thing all over again), I found this odd.
I checked out my TV show sync settings and noticed there were a bunch of missing episodes in the iTunes list as well as a bunch of others duplicated. It's really all messed up and mixed up. At this point I'm pretty freaked out as I paid a lot for these seasons. I went into my iTunes media folder and found everything to be right as rain. The shows are all present and accounted for - also within their correct season folders. I am pretty confused at this point.
I checked my other TV shows to see if the problem repeated in other places. I'm not a good test bed since I don't have a whole lot of TV shows on iTunes.
Firefly (season 1, only season) was fine
Random episodes (no more than 3 each) of Haven, Mentalist, The Shield, Sons of Anarchy, Stargate Atlantis, Stargate SG-1 were all fine.
Warehouse 13 (Season 4, only season I own) were all fine
The League (Seasons 1 and 2 - complete) were mixed up as well. Lots of duplicates in Season 1, many missing in Season 2. iTunes media folder is again, fine.
So, now I think this potential iTunes 11 bug occurs when you have multi-season TV shows in iTunes. The program isn't categorizing the different seasons properly in the GUI library.
Please help.

I'm having the same problem too, although it's with training videos that weren't downloaded from the Apple Store. I'm going to figure it out and re-post here soon.

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