Video changes after applying text track

Has anyone here seen this problem.
I work for education, so by federal law we must caption all video used by students. The problem I'm encountering is that when I apply a text track to a QT file, so that it is captioned, it changes the video track, so that the color doubles and the contrast of the image darkens.
If I turn off the text track this problem persists. If I extract the video from this file, (using the extract track option) into a new movie, (no text track brought over from the old movie) the video is fine again, till I add a new text track, then the whole problem presents itself again.
Has anyone seen this problem and if so, is there a soultion?
This also happens, if you apply a chapter text track as well.

Thanks for the resonse
The files are generated from an uncompressed 10bit video file, (exported out of FCP) and encoded, using Cleaner 6.5.
Chapter, (added in FCP) and captioning, (via Mac Caption Pro software) is added to the file, via text tracks, to the origianl video. These tracks are turned off prior to encoding the QT streaming files. But the data is transfered to the final QT streaming file during the creation of the steraming file.
All settings are set at default, the videos transparency is set to "None (allow dithering)" Layer 0. I've never change any of the settings of the tracks from there default settings.
To see this issue on your end, just extract the video from one of your current QT files, which will open it into a new window an compare the two videos at the same frame. More than likely, you will see what I'm seeing. Once a text track has been turned on, unchecking it will not return the video to normal, only extraction of the video to a new movie will reveal the original state of the the QT video.
Let me know what you find, thanks!

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