Not all rechargable batteries are the same. If you are using a battery pack designed for the wiimote, it shouldn't have that issue,
unless it's some el cheapo replacement that is simply a housing with 2 rechargable AAA NiCd batteries in it.
Maybe the remote measuring circuit isn't very accurate, and another remote wil last longer before it shows the low battery warning.
It might perhaps be possible to make a hack that forces the battery level as being full all the time. Since not many people complain,
I doubt someone will invest his time in this.