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OVRD_ALERT bit is being set due to fact there is some residual voltage on the ALERT Pin. 2.5V voltage on ALERT is a solid logic high. ALERT pin response could be due to a spurious glitch coupling onto the ALERT pin.
change out the 1Mohm to ~500K to GND. Also add a 470pF cap to GND.
make certain, the SYS_CTRL registers are cleared. to CLEAR write "1" in the corresponding register.
