"they still report the amount of charge correctly" ... "they never show the battery as full when the batteries are fully charged"
Seems there's a contradiction here.
Sorry, I didn't express well. Here, If I put a pair of batteries, fully charged, the wiimote will report 3 bars (instead of 4), but from here it'll update the indicator somewhat accurately (dropping to 2 bars, then 1, then it'll turn off). After the wiimote turns off, if I check the charge of these batteries in another device, they'll be very low, like the wiimote reported. In other words, even if my wiimotes doesn't show my Eneloop batteries as fully charged (4 bars), they'll update the indicator properly, somewhat accurately to when the batteries are at 50% charge or almost empty...
It seems updating to 4549 has solved the problem thus far. I'll reply back if there are any issues