This is the footage that goes into my software:

This is the footage that exports out of my software:

I'm sure you notice the line issues, but if you cannot see it, look at the line directly under the blonde haired girl's neck.
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I don't use any scripts (this is from a MEP, everything just imports directly into the software), and everyone used the same FPS/video size and type of footage, which I match on the export settings. I get this same effect when I export it as uncompressed, lagarith and UT.
Any assistance would be very greatly appreciated.