BQ76940: Alert pin not responding and other

Hi Tony,
1. Suggestions: Be sure the bit is being written successfully, read back the SYS_CTRL2 register to see if the bit is set.
Be sure you wait long enough for the pin to respond. The scheduler runs at a 250ms cycle, the write will be asynchronous to this so it may take up to about 500ms to see the ALERT go high.
The CC_READY bit in the SYS_STAT register also goes high when the result is ready, check to see if this bit gets set. When using CC_ONESHOT CC_READY must be cleared, but you indicate CC_EN which does not need the clear, however if you clear the bit you can see it set again.
Check that the ALERT pin is not held or shorted low by the host or other circuit.
2. I don't know the reference to R1 and R2. If these are the RGS resistors on the board, changing the discharge FET RDS resistor should not make a difference in operation since the part drives DSG high and low. Changing the charge FET RDS resistor may have a significant effect since the CHG pull down is weak and the smaller resistor will turn off the charge FET faster. The drawback to the 100k resistors is since the DSG and CHG are regulated to approx. 12V the current will be about 120 uA per resistor when on.
Also check the ground between the IC and the current path. We normally expect ground to be at the sense resistor, typically at the cell side, this gives a relatively low impedance path for the discharge FET drive.
3. If 2 boards of the same design vary in performance, look for assembly or component differences. If the difference is in the load current, check for loss across the FETs and possible voltage loss of difference between the IC and the FET. Also look for loss across the sense resistor or connectors.
If the difference is in the supply current, check for shorts across capacitors or look for high voltage across the IC filter resistors indicating a significant current into the IC or power net for the IC.