ITunes won't recognize some videos

I've been using a program called "ImTOO iPod Movie Converter" to convert video files to iPod format, but I'm finding that some of the videos won't go into iTunes. For instance, I encoded several videos all in one batch so they used the same default encoding settings, but only about half of them could be imported into the iTunes program. The ones that were recognized seem random, not in any kind of order.
Is there a reason why this happens? The ones that transfer to iTunes will upload to the iPod just fine, and they play the way they're supposed to. How do I make the REST of them work?
Custom   Windows XP  

OK, the first reply actually wound up working afterall. I don't know what I was doing wrong the first time I tried. I think it was because I was double clicking and all I apparently needed to do was click once. Thanks to all who replied!

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