NVRAM is corrupted when you replace the batteries.
All you need is a clear card (which anyone with a WMS machine should always have) and boot the machine with only that card in the OS CF card slot.
That simply boots an OS with the clearing code, and resets the machines NVRAM and tells you to power off when it's complete.
Then you just replace the original OS and Game CF cards and power on.
It will reload the OS and Game, and you just set the game options again and done. Machine is as it was.
There are many youtube videos on clearing and reloading/reconfiguring your machine so all is normal again, as long as you have (or get) a clear card for your machine.
If you need one post a WTB in the Classifieds section. There are many who can sell you one if you need. About $30 I'd guess is a typical price for a BB2 clear card.