New Computer - Updated iPod - Syncing Issues

Greetings!
I bought a new computer in January. At that time, I transferred my songs over to my new computer from my old computer using a cross over cable. At that point, both of my iTunes libraries were the same.
Since then I downloaded more songs and updated songs in the library, so I decided to finally sync my iPod classic to the new computer. I knew that I would have to restore the iPod, but since the libraries were the same, there should be no problem, right? Wrong!
Before erasing the iPod and syncing the songs, I stupidly decided to upgrade the software for the iPod (which I haven't done since I got it, due to reading related problems on here). So that goes fine and erase the iPod. Now on to syncing the library.
All the songs sync perfectly. The problem is with my video files. I had these movies on my iPod before I updated and erased the iPod. But now, iTunes says that the files are incompatible! I do not understand since they worked perfectly fine before! What happened?
According to iTunes they are MPEG-4 video files. The movies were made specifically for an iPod, so I do not understand what is going on. I figure that it might be due to the upgrading I did, but when I restore the iPod it always comes back with the same version (since there was no previous version on the new computer).
Is there a way I can fix the MPEG-4 problem or download and install the previous versions of the iPod software since iTunes does not give me an option? Should I try going back to previous version on my older computer (will this even work)? Mainly I would like to know why the MPEG-4 file that worked perfectly before is giving me problems and if it can be fixed.
Thank you!
(a frustrated) Lindsay

2/Downloaded 3rd party software to sync and install library from ipod touch into itunes on new computer.
You should have just copied \Music\iTunes\ folder from the old computer to the new computer.
but I can't get all of my applications and some bought items to appear on ipod
Connect thr iPod touch and select it in iTunes.
Click the Applications tab across the top.
Tick the apps you want to install onto the touch.

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