Rotation metadata is one of the first things I would check. Some cameras store orientation as metadata rather than physically rotating the encoded pixels. A proxy generator that bakes one interpretation into the new file can disagree with the original.

Also compare exact frame dimensions and pixel aspect ratio. A proxy should be lighter, but it still needs a predictable geometric relationship to the source.

I would test whether the problem follows the proxy file outside the editor. Open the proxy by itself and note its dimensions and orientation. If it is already wrong there, regenerate it with a different preset.

If it looks correct alone but wrong only when attached as a proxy, the issue is more likely the relink/mapping logic or a transform being applied twice.

In VSDC or any editor with automatic proxy management, I would avoid manually replacing the original clip with a random low-resolution export. Let the proxy mechanism maintain the association when possible.

For a custom proxy, keep the duration, frame rate and orientation behavior consistent. Then verify that switching back to the original does not change framing. A proxy that makes editorial decisions for you is not a transparent proxy.

I checked the bad files and the portrait proxies were physically landscape with a rotation flag, while my other proxy preset baked the rotation into the pixels. That explains why only one batch was inconsistent.

I am going to regenerate that folder with a single preset rather than fix each clip on the timeline.

Good catch. This is also why I keep proxies disposable. If a proxy has the wrong geometry, rebuild it; do not compensate with permanent crop/rotation changes that will later affect the full-resolution source.

The source should remain the authority for final framing.