You're right, you wouldn't expect both going bad at exactly the same
time. If you've always balanced the load between them, they'll wear
out at approximately the same rate, but wouldn't expect quite that
degree of synchronization.
Maybe the charger circuit is not adequately charging them?
Maybe the charge detection (probably by measuring battery voltage) has
gone bad? (Which could also lead to the charge stopping too soon
because it thinks they're full.)
You might try seeing how long one of those "5%" batteries will
actually provide power. One full discharge shouldn't unduly damage
them, and if you got 6hr or so that would prove the level shown was
Do they show the same 5% whether they're in the computer or out if it?
FWIW, charging to 100% isn't real good for Li batteries, they do best
if you avoid that last 10% full & empty. NiCd likes to be fully
discharged once in a while, and just topping off can lead to "memory
effect" reducing the amount of charge it will hold, but your computer
probably isn't so old as to have NiCds. NiMH have a normal
self-discharge of about 1%/day, and may need a full discharge/recharge
if they've been out of use a long time.