On Deck always shows latest episode of series to check into not last marked episode
I honestly don't even know if I'm describing this correctly but I shall try. I don't always watch shows from the first episode, especially if watching on TV. For the past month, when I check into a show that I have watched previously, if I check into an episode that aired BEFORE the episode I just checked into, it always shows the episode AFTER the one I checked into long before.
For example: I checked into The Andy Griffith Show episode 8x24 then started watching the show again from Season 1 and checked into episode 1x01 but my Recently Watched On Deck still shows 8x25 is the next episode I'm supposed to watch meaning I have to check on the episode, go back to Season 1 and pick the episode from there. It will constantly show 8x25 as the next episode to watch until I get to that episode which is about 200 episodes away.
Another example is The Great British Bake-off. I previously watched Season 5 but my PBS is now showing Season 4 so I checked into episode 4x01 but my On Deck is showing the next episode I need to watch is 5x11.
Example:
Deck shows: http://i.imgur.com/4Z9Ik0m.jpg
Recently Watched shows: http://i.imgur.com/u99FtT7.jpg
In my opinion, it would be much easier to use the Recently Watched On Deck section if it would always show the next episode (if it has already aired) that comes after the one you've recently watched/marked and newest one you've watched from whatever season is newer. Especially if it's a daily show like a news program, soap, or talk show that some people don't watch every episode of, but watch on a semi-regular basis.

This is currently as designed, but something I will revisit in the future.
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dgw commented
I have this issue with Last Week Tonight. I've watched some of the current-season episodes, so my On Deck is 3x06. But I'm primarily watching from the beginning, so it would be great if On Deck would actually show 1x23.
If I tell Trakt that I've watched all of Season 3, On Deck does correctly display 1x23 as the next episode to watch. But it seems to be using the first member of the last range of unwatched episodes, which is kind of counterintuitive.
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Hannah commented
I agree this is a great idea. I am currently watching The X Factor UK, and I have not watched the first editions, only the last 6, so my deck shows me 01x01 to watch, but I would like it to show me the episodes from the series that is airing now (12th). It is always on my deck -.- so I had to hide it. It would be way better if it appeared on my deck only on Mondays, after the new episode had aired and were pending for me to watch. I also had to remove American Horror Story from my deck for the same reason. I had only watched the series 4, and am now waiting for the 5th, and HAVE NO INTENTION of ever watching the previous ones...
My idea is: maybe it would be nice if we could personalise in a more advanced way our deck settings. So we could choose if we wanted it to show the next episode on deck to watch based on a) our latest watched episodes or b) oldest episodes that are pending.