I would say your new batteries might now be making good contact.
Happens to me all the time.

It was working before with the new batteries?
Those batteries should fit kinda snug.

Here’s some good info from pinwiki.

1.3 Settings Not Held or Battery Depletes Rapidly

A WPC MPU board with D1 and D2 circled. D1 and D2 are in the identical location on the WPC-S MPU

A WPC-95 MPU board with D1 and D2 shown in the middle of the picture, just below the battery holder
During the process of installing a remote battery holder, it is a good practice to check the diodes utilized in conjunction with the battery power. Diode D2, a 1N4148, is used to keep the MPU board's logic power from charging the batteries in the battery pack. Diode D1, a 1N5817, is used to keep the battery pack from powering the entire MPU board when the games's power is turned off.
If D2 fails shorted, 5VDC power will be applied to the batteries while the game is turned on. The end result is batteries which die prematurely, possibly leak, and/or possibly explode (alkaline batteries do not like to be charged).
If D2 fails open, the batteries will not power the static RAM, and the "FACTORY SETTINGS RESTORED" message will be displayed when the game boots.
Should D1 fail, the batteries would more than likely just deplete prematurely.

Probing pin 28 of the WPC-95 MPU RAM IC for Vbb (battery backup power)

Pinout of the 6264 RAM. Note Vcc, upper right, pin 28

Testing to see if battery backup power is reaching the RAM with sufficient voltage is easy.
Set your DMM to DC Voltage
Connect the black probe to game ground (in the picture at left, a clip lead is attached to the ground screw)
Use the red lead to probe pin 28 of the RAM
Measuring in this way should yield over 3.5 VDC. If measuring shows 0 VDC, either the batteries are dead, or D2 has failed (see above).
Ideally, this measurement should yield 1.5 VDC * 3 - .6 VDC = 3.9 VDC. This calculation represents the nominal voltage delivered by a single AA battery, times 3 (batteries), less a typical .6 VDC drop across diode D2. Remember that nominal voltage drop across a typical diode is .5 to .7 VDC.
6.12 Replacing the CPU RAM with non-volatile RAM

A WPC-089 MPU board with 6264 RAM, jumper W3 removed, and R93 in place.

A second option is to replace the 6264 static RAM with an NVRAM such as the RAMTRON FM1608 (or FM16W08). NVRAMs in the standard DIP package are becoming hard to find but several pinball parts vendors sell a nice 6264 replacement NVRAM based on these parts.
This method requires desoldering the OEM RAM from the board, and installing a socket on the MPU. Using NVRAM also has the down-side of not maintaining the Real Time Clock. This is meaningless in some games. But some games use the Real Time Clock, like Twilight Zone which moves the playfield clock to the current time of day during attract mode, and Who?Dunnit which has a "Midnight Madness" feature. Note: the WPC MPU is designed to accept either a 6264 or a 62256 static RAM. See: Jumpers, RAM and ROM size for a description of jumpers required when installing a new RAM or NVRAM.

40258D2C-9185-493D-AE45-0E595DB08C71 (resized).jpeg

Looks like something suspicious is going on around the two diodes that form part of the battery backup circuit. I would be investigating those before doing much more.

I would try putting in the batteries, then use the schematic to measure the voltage they’re supplying to other parts of the board.

Jeff