Make sure the square contact part (under the battery) is the correct orientation. Make sure all the correct screws are in to push the battery into this, and hold the plastic cover over this (without these, it will not recognise battery).
Get a schematic and board view, and measure R5280 and R5281. Check the voltage line from the battery to the logic board, chances are something is burnt or blown. Follow the voltage from the battery until it is not present, or see if something is shorting this to ground.