I personally don't like the sound of a motherboard that smells like it's been cleaned with chemicals. It may however, just have sat for a long time in someone's home who uses a strong laundry detergent that lingers in the air. It would make sense that the dust particles in the fan particularly have a strong scent.
The only thing I would use on electronics is denatured alcohol, which evaporates quickly and shouldn't leave a smell. If the smell is more like an abrasive chemical cleaner and strong across the entire board, I personally would return it. Even small amounts of liquid can cause corrosion that manifests problems later down the road.