Cannot sync iTunes U lecture videos to iPad Air

iTunes U lecture video link
https://itunes.apple.com/us/itunes-u/image-processing-reconstruction/id547294162 ?mt=10
I have this problem that cannot be fixed, no matter what I tried.
For most of the videos downloaded from iTunes U, I can sync from iTunes in Windows 7 to iPad Air fine. However, the videos from the link above can only be synced for the 2nd lecture while the rest have the error "were not copied to the iPad ... because they cannot be played on this iPad".
So, I tried to convert first using iTunes, make iPad version. That didn't work.
I downloaded Handbrake and used the preset "iPad" and "Universal", and that also didn't work. (at this point, I tried to encode using Handbrake with different presets for at least 4 hours).
It keeps saying "... because they cannot be played on this iPad".
So I tried to do the last thing on my mind, download the video lectures directly through my iPad. It worked, it kept the all the files (except the 2nd lecture which is "Processing" indefinitely, ironically).
However, the next time I synced it with iTunes to transfer more files (PDFs), the video lectures downloaded directly were wiped since it didn't download it through iTunes (the first time it copied the files from iPad to iTunes while the second time it wiped the video lectures from my iPad, except for the 2nd lecture that can be transferred).
My problem is... how is it possible that iPad can play the file yet iTunes still report an error that it cannot be played? Please keep in mind I tried re-encoding it numerous time already.
How can I keep the video lectures file on my iPad without downloading it through my iPad everytime I want to watch it after I sync my iPad with iTunes?

Stumbled onto information from another forum. MAYBE this is the problem, but what are solution options? What I did confirm is that ALL of the podcasts and iUniversity files that will not sync are MPEG 4 files. Let me know your thoughts.
Taken from another conversation to someone having a similar issue:
I just downloaded a full HD podcast video from iTunes to my iPad and desktop computer. Both of these videos play just fine. When I synced the iPad to my desktop computer iTunes would not transfer the video to the iPad. The video is 1920x1080, this outside the guideline for iTunes to transfer the video to the iPad.
The iPad is capable of playing a 1080p videos. When i need to send a 1080p to my ipad I use the GoodReader app to do so. It is iTunes (on the desktop) that is placing these restrictions on the videos that can be transfer to the iPad.
If you want to you can voice your opinion to Apple:
http://www.apple.com/feedback/ipad.html
*H.264 video up to 720p, 30 frames per second, Main Profile level 3.1 with AAC-LC audio up to 160 Kbps per channel, 48kHz, stereo audio in .m4v, .mp4, and .mov file formats; MPEG-4 video, up to 2.5 Mbps, 640 by 480 pixels, 30 frames per second, Simple Profile with AAC-LC audio up to 160 Kbps, 48kHz, stereo audio in .m4v, .mp4, and .mov file formats; Motion JPEG (M-JPEG) up to 35 Mbps, 1280 by 720 pixels, 30 frames per second, audio in ulaw, PCM stereo audio in .avi file format

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Cannot sync iTunes U lecture videos to iPad Air

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