Whenever I try to watch videos through iTunes, the audio goes out of sync. If I open up the file in QuickTime, the problem disappears, but it is annoying to have to open everything one-by-one in QuickTime. I *think* I have found a solution.
1. Close iTunes, Quicktime, and any other media-playing software.
2. Check your QuickTime settings.
Even though this is a problem with iTunes and not Quicktime, the problem may be solved by making sure your iTunes audio settings match your computer settings. Open QuickTime, go to QuickTime Settings, go to Audio, and under Audio Out, check what your settings are. They should be something like 16 bit, 44.1khz.
3. Check your speaker settings.
Open up your speaker settings and make sure they match your QuickTime settings. They should be something like 16 bit, 44100 hz (CD Quality). If they do not match your QuickTime settings, change them.
4. Start iTunes.
Open iTunes again and see if the problem is fixed.
This seems to have fixed the problem for me. Please mention in the comments if it works for you.
Source: iTunes Forum