QuickTime stutters only with .mpg files

Only since I've updated to Mac OS X 10.5.2 that I've been experiencing this problem. I have a load of .mpg files recorded using my digital camera, as well as a bunch of files I've downloaded from the net. These used to play back perfectly fine and smooth in QuickTime, but now every few seconds there is a big stutter. The files aren't corrupt as every other media player plays them fine. Also, it is just .mpg files QuickTime is struggling with, any other supported format plays perfectly fine.
The file codec is 'MPEG1 Muxed'.
I've tried reinstalling QuickTime, the Leopard Graphics update and neither have provided me with any fixes.

Why did you uninstall Perian? You need it!
These are the downloads and the settings you need in order to view/hear pretty much everything that the net can throw at you: The setup described below has proved repeatedly successful on both PPC and Intel macs, but nothing in life carries a guarantee!
It is known to work in the great majority of cases with Safari 3.0.4, QT 7.3 or 7.4 and OS 10.4.11. (If you are running Leopard, ensure that all plug-ins have been updated for OS 10.5.2, but please see my footnote).
Assuming you already run Tiger versions OS 10.4.9 or above (this has not yet been verified with Leopard) and have Quicktime 7.2 or above, and are using Safari 2 or 3, download and install (or re-install even if you already had them) the latest versions, suitable for your flavor of Mac, of:
RealPlayer 10 for Mac from http://forms.real.com/real/player/blackjack.html?platform2=Mac%20OS%20X&product= RealPlayer%2010&proc=g3&lang=&show_list=0&src=macjack
Flip4Mac WMV Player from http://www.microsoft.com/windows/windowsmedia/player/wmcomponents.mspx (Windows Media Player for the Mac is no longer supported, even by Microsoft)
Perian from http://perian.org/
You should read this support page http://perian.org/#support in case you need to delete older codecs.
Adobe FlashPlayer should first be uninstalled using the appropriate uninstaller available here: http://kb.adobe.com/selfservice/viewContent.do?externalId=tn_14157&sliceId=2 and then the latest version obtained from here: http://www.adobe.com/shockwave/download/download.cgi?P1ProdVersion=ShockwaveFlash and installed.
(You can check here: http://www.adobe.com/products/flash/about/ to see which version you should install for your Mac and OS, but please see my footnote if you are running Leopard.)
In earlier versions than QT 7.1.3 in Quicktime Preferences, under advanced, UNcheck Enable Flash, and under Mime settings/Miscellananeous only check Quicktime HTML (QHTM).
You should also ensure, if you are running Tiger 10.4.11 or Leopard, that you have downloaded and installed the correct version for your Mac of Security Update 2007-009.1.1, which also deals with the Quicktime/Flash issues you may have experienced, such as the '?'. What happened was that both Quicktime as well as Adobe FlashPlayer tried to play the Flash video at the same time. This no longer happens. (N.B. Security Update 2007-009 1.1 requires both a restart and a permission repair.)
If you get problems with viewing video on a website try moving this file to your Desktop:
Hard drive/Library/Internet Plug-Ins/QuickTime Plugin.webplugin
and then restarting Safari. If all now works, you can trash that file.
In Macintosh HD/Library/Quicktime/ delete any files relating to DivX (Perian already has them). However it should be noted that Perian is not an internet plugin and will not play DivX files imbedded on a website. For that you will need the DivX Player browser plugin available from http://www.divx.com/divx/mac/
Now go to Safari Preferences/Security, and tick the boxes under Web Content (all 4 of them) to enable Java.
Lastly open Audio Midi Setup (which you will find in the Utilities Folder of your Applications Folder) and click on Audio Devices. Make sure that both Audio Input and Audio Output, under Format, are set to 44100 Hz, and that you have selected 'Built in Audio'.
Important: Now repair permissions and restart.
You should also consider having the free VLC Player from http://www.videolan.org/ in your armory, as this plays almost anything that DVD Player might not.
FOOTNOTE
If you are running Leopard:
Some users have mentioned that the latest Flash Player (v.9.0.115.0) conflicts with Leopard, and that they have needed to revert to v. 9.0.47. This can be downloaded from here:
http://kb.adobe.com/selfservice/viewContent.do?externalId=tn_14266&sliceId=1

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