The 1099-S indicates that you sold the property. You then used that money plus additional funds to purchase a new place. Taxes are due when you sell one of your homes. The fact that you rolled the money into a new home doesn't negate the fact that you sold a home. The fact that you have 3 1099-S forms indicates you have multiple homes and sold 3 of them.
Next time you do this with property, look into doing a 1031 exchange so that the tax is delayed until the sale of the new place.
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