Ah... that could be the problem! Can you measure the voltage at the NVRAM?
From the schematics, you can see that 8.2V supplies the voltage for the chip, which gets dropped to +5V through a resistor and diode. This is so the chip still gets +5V with the voltage drop across the diode... if they connected it to +5V with a diode, the chip would only get 4.3V or so. The replacement power supply doesn't provide +8.2V, so they may have connected it to +5V, +12V, etc.
Assuming that you don't have +5V at the RAM, since you don't need the battery anymore, the easiest fix is probably to add a jumper wire simply connecting +5V to the NVRAM power pin.
Or, you could connect +5V to the battery '+' terminal, and jumper across the 270 ohm resistor R142.
DogP