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Welcome to the Forum, Macca.
You've got at least 2 different changes here - the change from Auto to Manual, and the change from JPEG to RAW. If in manual mode you're selecting a small aperture (f/22, say) that can cause sensor dust spots to show up. If that's not the problem, it may be something in the RAW conversion that's generating the artefacts.
Try shooting Manual with RAW+JPEG, and comparing the images side by side.
Post an image with the problem and we might be able to give better advice.
Chris
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