Nano and videos

G'day! I know this topic has probably been done to death, but I'm out of ideas.
I've had my 8GB Nano 5th Gen for a few months and everything is working flawlessly. There's just one thing I can't figure out.
I know that Nano supports .mp4 video files, and all the videos that I've added to my iPod are .mp4's. They're running perfectly.
I have an anime series on my external hard drive, they number 14 files and they are all .avi format. Using the same program that I used to convert my other video files, I have managed to convert all 14 .avi files to .mp4.
Now, when I tried to add these 14 files to my iTunes library to then sync to my iPod, all the files are added to the library except episode 5 & 6. I have tried reformatting these files into .mp4 again and even to .mov and adding them to the library, but they still don't show up. I thought maybe they weren't adding coz iTunes could see they wouldn't fit on the iPod, so I deleted some of my old videos to make space, but it didn't work. The converted videos that ARE showing up in the library are running well: they play when i hit 'play now' and i can rename them and everything.
when i watch the files as .avi's (in Nero Showtime), they run well and don't skip or malfuction at all.
So just to recap - I've successfully converted 14 .avi files to .mp4 but only 12 of them appeared in the iTunes movie library.
I am using a Toshiba laptop with Windows Vista. I'm running iTunes 9.
Thanks in advance!

hey planb77! thanks for the welcome, mate!
I'm using a program simply called Video Encoder. I downloaded it free from http://www.prvsoft.com/. I consider myself pretty compter savvy but encoding and translating and converting are still pretty new to me.
Video Encoder has a really simple, easy-to-use interface and all the videos that I've added to my iPod have been converted with this program. This is the first time this has happened, that the converted videos aren't showing up in the iTunes library.
When I use Video Encoder to convert Eps 5 & 6, it does it succesfully; it saves them to my folder as an .mp4. I've tried adding them to the iTunes video library but they don't come up.
I tried your suggestion of using the iTunes built-in converter but it's coming up as a gray colour on the menu so I can't select it. I've never actually used to iTunes Converter before.
I'm thinking if I should download a different converter. I don't have a credit card so I can't buy anything from the net, but I don't like doing that, anyway.
Till next time, mate! =)

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INTEL_ DG41RQ__
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Apple Application Support 2.3.6
iPod Updater Library 11.1f5
CD Driver 2.2.3.0
CD Driver DLL 2.1.3.1
Apple Mobile Device 7.0.0.117
Apple Mobile Device Driver 1.64.0.0
Bonjour 3.0.0.10 (333.10)
Gracenote SDK 1.9.6.502
Gracenote MusicID 1.9.6.115
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Default Gateway:     192.168.5.1
DHCP Enabled:       Yes
DHCP Server:          192.168.5.1
Lease Obtained:      Sun Dec 22 21:35:11 2013
Lease Expires:         Mon Dec 23 21:35:11 2013
DNS Servers:          91.216.105.75
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Online:                     Yes
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Using LAN:              Yes
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