iTunes library won't add / list several of my TV-Show episodes

I'm having great trouble with adding a few episodes from my TV-Show library into iTunes. I've been converting everything from MKV's containing Dolby Digital 5.1 (AC-3) and DTS into MP4's (M4V) containing Dolby Digital 5.1 (AC-3) with all kinds of metadata goodness and whatnot.

But upon adding everything into iTunes there seems to always be some hiccups no matter what I do.. Let's take my library of Family Guy Seasons for instance. I've got like five seasons of Family Guy, all in M4V files containing either 2.0 AAC or 5.1 AC-3 audio and H264 video all labelled correctly. After adding the folder to iTunes I notice that the entirety of most seasons are showing up correctly, but season 9 for instance only shows episode 8-X. The first seven episodes are not showing in iTunes whatsoever.. I tried to delete my entire library and add everything fresh but the same thing occurs no matter how many times I try. I even tried iTunes on a entirely different system, same results.

I can play the actual episodes using iTunes or QuickTime with no issues at all, I can even verify the metadata being correct, I try to manually add these exact episodes to my iTunes library but no, they are not showing anywhere and are not searchable in my library and therefore there is no way for me to get it playing using my Apple TV as it seems to be downright impossible to get them into my iTunes library.


It seems to happen with completely random episodes, there are quite a few Family Guy episodes missing in season 9, there are some missing in How I met Your Mother season 8, I'm missing quite a few in Lost season 5 and whatnot. But upon adding my TV-show library it seems to always be the exact same episodes within my series that wont show for some inexplicable reason.


Have anyone experience anything like this? How do I bypass this obscure problem, is there some other way for me to get things into my iTunes library so it gets available on my Apple TV?

It's mostly from my older library of Blu-Ray encodes from Blu-Ray discs into MKV files containing h264 video and Dolby Digital 5.1 or DTS 5.1 depending on the audio track from the original disc.

For remuxing my MKVs into MP4 I've been using MP4toMKV which simply unpacks the video and audio stream and repacks it into MP4 container, there is no converting or encoding involved unless the MKV has been featuring DTS which then have been converted to WAV(E) and then made into a 6-channel AC-3 (Dolby 5.1) track.


All metadata is pulled directly form IMDB's servers and provides near perfect metadata all the time.

Seems like I have managed to solve it by being in the respective TV-Show and Season folder while manually opening the missing episodes in iTunes they get added to the list. There are still something fuzzy about a few episodes, but I'll try to redo the metadata of those and see if that might help.

None is shown under "Home Videos", however as I mentioned I've managed to get most of them working now after manually navigating to the correct season, under the right series and then manually opening the M4V files missing.

Now I've got only one season not showing correctly, LOST Season 03.. This one is completely off, it doesn't show the first six episodes of Season 03 but all the other episodes from season 01 throughout season 06 is showing correctly.

I tried to redo the metadata on the first six episodes of season 06, but they still wont show no matter what I do. The weirdest thing with these episodes is that when I manually play the M4V files using iTunes, iTunes recognise them as LOST Season 02 episodes and not Season 03 episodes. So LOST Season 03 - Episode 01 which is "01. A Tale of Two Cities" is shown as LOST Season 02 - Episode 10 which is "10. The 23rd Psalm". That's quite odd, which was the reason why I went ahead and rework the metadata of these episodes just to be sure.

But still it wont show in the iTunes library and when manually opening the M4V files with iTunes it still shown as being "10. The 23rd Psalm" instead of "01. A Tale of Two Cities". If I open the file with QuickTime Player, Windows Media Player or Media Player Classic Home Cinema they all list it as "01. A Tale of Two Cities" and not "10. The 23rd Psalm" as iTunes does. Watching the playback it's quite clear it's indeed playing back A Tale of Two Cities and not The 23rd Pslam episodes, even in iTunes.


I have no clues why iTunes is making a mess out of the first six episodes of LOST Season 03, it really doesn't make much sense as there is nothing with the M4V files, their contains or their metadata that points towards iTunes recognising it as a LOST Season 2 episode at all.


EDIT:

Just to confirm the metadata in iTunes I tried to remove the whole LOST series from my library and the go ahead and add ONLY the first six episodes of Season 03 and nothing else.. Then they are showing correctly, with the correct metadata for each and every episode.

But upon adding the rest of the bunch they disappear and suddenly iTunes starts mixing the first six episodes of Season 03 as Season 02 episodes...



EDIT2:

As soon as I add any episode of LOST Season 02, 10-15 they seem to replace LOST Season 03, 1-6. So Season 03 is working perfectly, having all the right metadata and everything but as soon as I add LOST Season 02, Episode 10, LOST Season 03, Episode 01 starts playing as LOST Season 02, Episode 10 and then disappears from the library. Upon adding and playing back LOST Season 02, Episode 11 it replaces LOST Season 03, Episode 02 which then disappears from the library and this goes on for episode 10-15 of Season 02 which for some reason replaces episode 01-06 of Season 03.