I never charge the batteries inside mine. Always take them out and charge them with an external charger. I've got 6 batteries that I rotate, and always keep the set outside the scanner fully charged and ready to go.
Do yourself a favor and turn off the scanner's built-in charger, and get yourself an external charger. The scanner has no smart charge circuitry at all, meaning it doesn't charge each cell individually, nor does it have any clue when each cell is fully charged. The $20 you spend on a decent smart charger will give you peace of mind knowing that an overheated cell, burst cell or worse won't destroy your $200 scanner.