Convert Selection for iPod/iPhone Not Doing Anything

I have a ton of TV Shows that I ripped from my DVDs using Handbrake and put into iTunes. When I was ripping the videos, I chose to use the Apple TV preset since that is what I am mainly using to view the episodes. However, I have found that files created with this preset are not playable on the iPhone. I tried using iTunes' "Covert for iPhone" feature, and the file looks like it is getting converted, the progress bar goes all the way and the little success sound is played, but the file is still unable to be synced to my iPhone.
Has this happened to anyone else that was able to find a solution? The only thing I can think of is to rerip all the episodes using a preset that is playable on the iPhone, but that would be a real pain since I have about 600gb of video files to rerip...

Thanks for the reply, but iTunes did not create a new file. I looked in Movies and in TV Shows, and in Music just to be careful, but there is still only one file, the one that doesn't play on my iPhone. I even looked in my iTunes Music folder for a file it may have created an just not imported, but there is nothing there either.

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