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The programing resistor (R1) goes to VSS (not Vin), so that needs to be corrected. Keep in mind that the part number has an extension that is unique for the battery chemistry. The part that you need for Lipo is MCP73831-2 (4.2V end voltage). I have used this chip a lot on consumer products and I have found it to be very sensitive to input voltage. Be careful to minimize the input resistance (heavy gauge wires or think traces if on a PCB).
Thanks for the input