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I think I solved it by disabling the shadow edit file and the continuous thumbnail image. So far so good.
None of those is related to the content of actual frames. The continuous thumbnail feature is only meant to give you an idea of what content is where in the clip, and unless you have the timeline zoomed in so that every single frame is visible it's possible that the thumbnail content won't line up exactly with the underlying frames.
Similarly, shadows files are created with the same frame rate as your original clips so using or not using them shouldn't have any impact on the contents of each frame. You may need to set the drop-frame option if you're working with 30fps or 29.97fps clips, for example.