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Can you create a simple sphere alongside your model about the same size and see if the sphere's vertices are displayed properly?
I can't see your settings in your post.Can you send me the model file and your whole config setting files?
In 'Scene Explorer > Retopo Reference List', either uncheck 'Retopo mode enabled' (Recommended since you have no retopo objects in the list) or reduce the z offset value.When 'Retopo mode enabled', selected objects will be rendered advanced in z to ensure on top of the reference object.