Quicktime Pro wont save video in rotated version, reverts to original.

Despite following all the steps to rotate a video saved from iphone 4 it won't save its new version (PC) ..have clicked save as , re-named file and it will save as a new file but it is still upside down in the thembnail and if you open it with any other media player (e.g) VLC it plays upside down again ...the strange thing is all upside down videos appear fine when Quicktime opens them but the thumbnails  and any other media format /player, recognise them as upside down ...HELP /explanations please

By export it work properly, but we lost main advantage QT,- speed. It one reason for me only for using QT as the editor... I have 264codec in .mov files from my camera. If I split them, merge, add music and text, that all need for home video. QT to make that operations in some seconds... But export proceed some hours!!
The export is only required if you are making changes like display rotation AND viewing the results in a non-QT media player like VLC. If you will be viewing the results in the QT media player only, then the quicker "Save"/"Save As..." option should play correctly.
May be you know as to accelerate export?
Export speed depends on the the settings used and the hardware involved. Using a newer, faster platform or using a hardware accelerator like the Turbo.264 HD is usually the easiest way to improve conversion speed.
That problem is valid not only for ROTATE, but for added MUSIC and TEXT  too.
Not sure about your problem here but this may be a problem with a straight "Save"/"Save As..." option not flattening track content. For instance, if you merge/add multiple audio tracks and then view the results in a media player or on a device that only plays one track at a time, then only the default track will be heard. (I.e., unlike the QT player which plays all "active" tracks in a file simultaneously.) On the other hand, the export flattens (combines) all of the audio tracks to a single audio track which then plays correctly in such software and on such devices.

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