PRAM batteries in those things are getting kind of old by now. They're little LiIon cells, in flat packs installed in the top case above the expansion bays (at least one - I don't remember if there are one or two batteries). If they're no longer charging properly, they may cause issues with the charging of the main batteries and the state of your PRAM settings. As others have suggested, you might try unplugging them if you can get at them.

However, sometimes the charge boards on those old 'Books die. The WallStreet, in fact, is notorious for charge card problems. I've seen several where they wouldn't charge the batteries at all, even thought the batteries were good. Other machines would only charge batteries if the machine was off or in sleep mode, not when it was running. Weirdness, and annoying to boot. Try seeing if the batteries in yours will charge with the computer shut down.

Finally, you can try the PowerBook G3 Battery Reset program. That may or may not be the original name, but you should be able to find the program without too much problem by searching Google or Apple's own website (it's an Apple utility). This utility has more than once been credited with resurrecting uncooperative batteries.