I do think that solving the duplicate seasons issue will also make the missing shows reappear. This is something at the Video App programmers need to fix (and have needed to fix for awhile), but if you want an immediate solution. The following steps might work:
1. In iTunes, go to your TV Shows and sort/group them by seasons.
2. For just the seasons that are showing up twice in the Video App, shift-click to select all the episodes for ONE of the problematic seasons.
3. Option-click (or right-click) the selected episodes, and select "Get Info" from the pop-up menu.
4. If asked, "Are you sure you want to edit for multiple items?", click "Yes".
5. In the Artist and Album Artist fields, type the show's name (for example, "Mythbusters").
NOTE: I believe that the Artist and Album Artist fields must be the SAME for all episodes of this show across all seasons!
6. In the Album field, type the show's name followed by its season (for example, "Mythbusters, Season 4")
7. Click on the Sorting tab.
8. In the Sort Album field, type the show's name followed by its season (for example, "Mythbusters, Season 4").
NOTE: I believe that the Album and Sort Album fields must be the SAME for all episodes within a season (but will be different for each season).
9. Close the Info window, and repeat for all other seasons that have duplicates on the video app.
It's still tedious, but at least you only have to make the edits for an entire season at a time, and only for the ones that are repeating themselves in the Video App.
Good luck!
Jonathan