TV Episodes Missing from Apple TV and iTunes

I believe this may be a cloud issue so I'm posting here.

I have various TV shows purchased from iTunes (access using my imac, iphone, ipad and PC laptop). I also just recently bought an AppleTV.

Some of my shows have 'missing' episodes and some have an entire season not showing up in my iTunes library on my computer/ipad or under 'purchased shows' on AppleTV. When I go to look at these missing episodes/seasons in the iTunes store, they show as purchased and they give me the option to download to my computer if I want; or I can watch them on AppleTV. So I know these shows have been purchased.

Here are some examples of what I'm dealing with:

Burn Notice, Season 3 - missing episodes 1 through 11

Burn Notice, Season 4 - missing episodes 2, 5, 7, 9, 11, 13, 15, 17

Modern Family, Season 2 - missing episodes 2, 16, 21, 22, 23, 24

True Blood - missing entire seasons 2 and 3

I have 116 'missing' episodes out of my total 1,175 TV episodes in my current library in my cloud.

Anyone know how to fix this? Ultimately it's not a huge issue since I can access the shows if I navigate to the store, but it's rather inconvenient, and since AppleTV doesn't list the episode #, I could easily miss watching an episode if I'm just rolling down the list of episodes in a show. I just want all of my purchases from iTunes to show up in my library and on my AppleTV.