Problems converting for iPod

I am sure this must be simple butttttt… can someone explain what the difference is in file types and format for the iPod. I have a large collection of DVDs which I have used DVD Shrink to convert to the muliple video files. Then I used Handbrake to try to convert for iPod. I have tried converting to MP4 and M4V. Both file types will play using QuickTime. And when I import the files into iTunes, they both will play. But when I drag them to my iPod, neither format will import. I get an error message saying the file is not being transferred to my iPod because it will not play on it. Is this a driver issue, a version issue on my iPod or some copy protection issue? Thanks for your help!!!