Stuttering sound and re-conversion is the system trying to make heads or tails of formats it has no codecs for. Most of what we use now is NOT of Apple's creation other than the .mov format, and that is a container for the audio and video!
You need to rebuld the libraries of codecs and DO NOT USE QuickTime Player X! Apple is going all gung-ho with security since the migration to the 'cloud' and computers are expected (eventually) to be online all the time. It's security, security, security, and since the QT technology IS a Core Component, it's becoming all firewalled (hence a lot of video formats not working on the QuickLook)
Stick to QT 7.6.6, it will run and accept all the codecs since it is not the 'officially' nested QuickTime player anymore.
Here is a list I'm putting up all over, since I've gotten my install of Mavericks to run flawlessly with all of my video.
Start with QT 7.6.6. - http://support.apple.com/kb/DL923
Get Perian, and install it. - http://perian.org
then VLC, - http://videolan.org
DivX - http://divx.com - and the
Flip4Mac package from Telestream - http://www.telestream.net/flip4mac/
This is what I've put into my system and so far I've gotten every file to run just ducky, even my oldest videos.
In System/Library/QuickTime
ApleIntermediateCodec.component (should already be there)
AppleMPEG2Codec.component (optional if you paid for it)
DivX Decoder.component
Flip4Mac WMV Advanced.component
Flip4Mac WMV Export.component
Flip4Mac WMV Import.component
In your Home/Library/QuickTime/
AC3MovieImport.component
Perian.component
For AC3 sound that is in most .mkv files, you need the A52Codec.component, here:https://dl.dropboxusercontent.com/u/34821905/A52Codec.component.zip - unzip the file and put the component into the System/Library/Audio/Plug-ins/Components..
Go back to your Perian settings and in the Audio Output button, set it to 'Multi Channel Sound' - Ignore the message Perian puts up and select it.
By doing a 'Get Info' on your files and where it says 'Open With', default them to the QuickTime 7 and set it so it is the default for all the files of whichever type you use. It should work perfectly. So far I've gotten ALL my old videos to play and not a one has wanted to reconvert, even my older .mov files.
Regards,
Deb.