[Rob Postroz] “The camera I shot the footage on was a canon xl1.”
The XL1 had a “Frame Mode” that was, frankly, not the best way to film on that camera. It was a workaround “de-interlacing” in camera (as opposed to the DVX100 which would give you an actual 29.97 progressive) that caused a resolution loss of around 25%, which I’m sure you’re already aware. However, the footage is still interlaced, not actually progressive. It’s simply trying to emulate the look of progressive within interlaced (as kooky as that sounds).
[Rob Postroz]I recall many years ago when working in an older version of FCP that these lines would appear when editing this type of footage, but the solution just seemed to be to check a box in the viewer (like view in highest quality or something).
Have you tried doing this in FCPX? There are similar options. I would also render out a section and see if it still looks the same.