The Power User's Guide to Video Encoding with Handbrake
Troubleshooting Tips

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My Video/Audio is Jerky and Skips Around
Start over. Seriously. it sucks to have to start an encode all over again, but there's no way to fix a choppy rip. There are a few different reasons why your rip may have turned out bad. First and foremost, make sure you're not trying to tap into your CPU's cycles while encoding. Ripping movies is hard enough on the processor, so let it finish before you load up those Photoshop scripts for that side project you've been working on.
Much more common is a bad setting or multiple bad settings in Handbrake. If you're using one of the preset profiles, this usually won't be a problem, but if you created your own profile, then something's out of whack. Reference the beginning of this guide for settings recommendations and explanations of what each one does.
It also doesn't hurt to see what settings work for others, and as luck would have, there's a pretty long thread in Handbrake's forums dedicated to this very topic. You can view it here.
Finally, if you're ripping a DVD, be sure you've installed a decrypter, such as AnyDVD, DVD43, or DVD Fab HD.
I Included Subtitles but They're Not Showing Up
Soft subtitles need to be turned on in your media player if you want them to show up. In Windows Media Player, press CTRL+Shift+C to toggle subtitles on and off, or press the Alt key to bring up the menu bar and navigate to Play>Lyrics, captions, and subtitles>On if available. In VLC Player, navigate to Video>Subtitles Track and choose the soft sub you wish to display. In QuickTime Player, you'll find the option under View>Subtitles.
I Don't Want Soft Subtitles. Can I Hardcode Subtitles with Handbrake?
Yes, you can. In the subtitles tab, before adding in a subtitle, check the 'Burned In' checkbox.
Audio and Video is Out of Sync
Sometimes the audio won't sync up perfectly with the video, and even minor delays can be both maddening and annoyingly distracting. Luckily, there's a free program that will fix this easily and quickly.

Download MKVToolnix from here and fire it up. Click on the Add button and select your out-of-sync video. Highlight the audio track and click on the Format specific options tab. You'll notice a blank field title Delay (in ms). Inputting a number here will push or pull the audio forward, depending on whether you input a positive or negative value.
AC3 Passthrough isn't Working on My PlayStation 3 Console
Sony's PS3 doesn't support AC3 in MP4 format, so you're going to have to remux the file. We like using tsMuxer for this, which will let you remux to TS or M2TS.