I had this same problem s a lot of others after updating to the latest I Tunes version. I finally got a decent response back from Apple, which was hard to do. Here is what they told me. Maybe it will help you:
I'm sorry to hear that you're dissatisfied with the way the episodes you purchased plays in iTunes on your computer. I appreciate your decision of contacting us to have this concern addressed. It's my pleasure to be of help for you today.
Raymond, please accept my sincere apologies for the inconvenience this issue has caused you. iTunes Store videos are optimized for playback on iOS devices and Apple TV.
This article often helps customers who are having video playback performance issues:
Troubleshooting iTunes for Windows Vista or Windows 7 video playback performance issues
http://support.apple.com/kb/TS1718
If your computer meets the requirements yet video playback is not satisfactory, here are some things that might improve the quality:
1) Make sure you are using the latest version of iTunes for Windows. It is available free of charge here:
http://www.apple.com/itunes/download
(Note that installing the latest version of iTunes will not affect your library or any items in your account waiting to be downloaded.)
2) Quit as many other open applications as you can before playing videos in iTunes.
3) Wait for all iTunes Store purchases to finish downloading before playing videos.
4) Use this article to guide you through updating your PC's drivers:
Updating the drivers on your Windows PC
http://support.apple.com/kb/HT1768
5) Disable all non-Microsoft startup programs and services by following the steps in the appropriate article below:
Using Msconfig to troubleshoot conflicts in Windows Vista and Windows 7
http://support.apple.com/kb/HT2292
6) If the video's audio track is not satisfactory, follow the troubleshooting steps in this article:
iTunes and QuickTime for Windows: Songs and other audio don't play correctly
http://support.apple.com/kb/TS1362