There is already a 1280x720 25 fps preset in Settings > Video Mode > Non-broadcast. Maybe there is something incorrect in your redundant custom preset. If you are changing the resolution or aspect ratio in Export, that is a sign there may be something wrong with Video Mode. With intimate knowledge of Shotcut internals, I struggle to understand how additional cropping is occurring. It does not do that. When things do not match up black padding is rather added. Otherwise, I do not use Rotate and Scale for this purpose.
- Start over
- Settings > Video Mode > Non-broadcast > HD 720p 25 fps
- open the video file
- add the Crop: Source filter
- click the Center checkbox in the Crop: Source UI
- Export, do not click anything in Export except Export File