Yes, the 3AA batteries are for storing your settings and high scores.

Is this a new issue or has the game behaved this way since you got it? (congrats btw)
Do you have a multimeter?

Batteries dead?
Batteries in wrong?
Batteries leaking?

In the near future you can install a remote battery pack or NVRAM to avoid leaking battery disasters, but for now I would read up here:
http://www.pinwiki.com/wiki/index.php?title=Williams_WPC#Battery_Issues

Especially the part (at 5.10.3) about testing if your battery voltage is reaching your game RAM.

Also, maybe check out your local pinsiders, maybe one of them can help if you have trouble solving this:
https://pinside.com/pinball/map