So he's putting the battery back in while the computer is ON?
He says the battery reads 3V, but given the load shown below, I'll bet it drops below 3.0 when installed. For $3-4, try a new battery.
Intel® Desktop Board, D945GNT, Technical Product Specification
1.5.4 Real-Time Clock, CMOS SRAM, and Battery
A coin-cell battery (CR2032) powers the real-time clock and CMOS memory. When the computer
is not plugged into a wall socket, the battery has an estimated life of three years. When the
computer is plugged in, the standby current from the power supply extends the life of the battery.
The clock is accurate to ± 13 minutes/year at 25 ºC with 3.3 VSB applied.
NOTE
If the battery and AC power fail, custom defaults, if previously saved, will be loaded into CMOS
RAM at power-on.