Stuttery, Pixellated visual playback

I have posted this problem before and no one seemed to know how to fix it. I thought i would wait for an itunes/Quicktime update but that did not solve the problem so I am posting again.
When i try to watch a video file through quicktime or a video podcast via itunes the Visual part of the playback stutters, pauseing for seconds before showing the next image which may or may not run normally for a second or so before doing the same. Often the transition from one image to the next causes the image to pixellate. The sound however is perfect throughout.
What is confusing though is that i can watch video files on websites such as gametrailers.com that use quicktime and they play perfectly.
Having looked at the Show Movie Inspector panel in Quicktime, the counter reading does not run sequentially, it seems to run as if being in fast forward skipped 20-40 seconds at a time.
I have tried everything i can think of and that has been suggested to me and the problem still persists.
My drivers are up to date, Quicktime is up to date, Quicktime Alternative suffers the same problem, I have tried uninstall/reinstall.
I have an NVIDIA GeForce 7900, running Windows Vista.
Message was edited by: Ednory
Message was edited by: Ednory

I have found something of interest, http://www.geekzone.co.nz/hadders/2273 is a forum thread of someone having a similar problem that he linked to Intel RAID array. I have no idea what that is, i have an AMD Athlon and a single unpartitioned internal HDD and an external one.
But the second post made a suggestion of running the file from an external HDD, which i did and which solved the problem to an extent.
It is now a task of finding out what is causing .mov files played from my internal HDD to play in this manner. It used to play them perfectly fine untill a number of months ago.

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