QuckTimeX cannot seek within video files after corruption

I have recently encountered a problem with playing a couple video files in QuickTimeX. Recently, the USB Hard Drive that contained the video files had a error, and the video files were corrupted. They were recovered using chkdsk utility on my windows laptop, as well as the other files that were corrupted, but under QuickTimeX the video files only load the first ~4 seconds of a 20-40 minute video.
Video files that were corrupted are both .avi and .mkv type files, QuickTimeX plays using Perian plugin. I've tried these video files on another Mac, without success; however they work on my windows laptop.
After looking around, I found MPlayerX and tried to play the video files, and they worked fine.
This makes me believe there is something wrong with the way QuickTime reads the file or how it tries to index/seek within the video.
I'm not sure where to go from here, and any information you could provide on what the exact problem might be and how to fix it would be much appreciated. If there is any more information you need I will gladly attempt to answer to the best of my ability.
Thanks in advance,
David.

This makes me believe there is something wrong with the way QuickTime reads the file or how it tries to index/seek within the video... I'm not sure where to go from here, and any information you could provide on what the exact problem might be and how to fix it would be much appreciated. If there is any more information you need I will gladly attempt to answer to the best of my ability.
Can't really help you with a solution but can confirm that QT does look for a formal physical termination of content unlike Windows which is "stream" oriented, taking data and playing it as it may (or may not) access it. QT, on the other hand, either expects to immediately know where the termination is or, with some files like MPEG (MPEG2/MP2), will trace/load the entire file to get this information before even beginning playback. In most cases, improperly terminated files will not even open in QT applications. I suspect that whatever you did to recover the files on the Windows machine effectively turned the files into something QT apps see as a "segmented" file in which the first segment is seen as an independent, closed/properly terminated file. (I.e., as seen on many PC video web sites where PC users segment their files for sequential uploading as multiple files but which the QT browser software will only play the first segment properly.)

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