Have you waited a few minutes, to see what the charger does?
The charger can only recognize the chemistry by what the initial voltage is. For example, if the cell is 3.0v, then the charger knows it is lithium-ion. If it is 1.0v, then it assumes it is NiMH. If the battery has very low voltage (I forget the amount, but something like less than 0.5v), the charger doesn't know what the chemistry is, because it could be a depleted lithium-ion or NiMH.
So, the charger does a slow-charge for awhile, assuming it is lithium-ion. This is maybe what you are seeing. After a few minutes, if the voltage rises above something like 2.0v, then is knows it is lithium-ion and proceeds as normal. But if the voltage never gets above something like 1.5v, then it assumes it is NiMH and will switch the charging algorithm to NiMH. When that happens, you should see the charger change the chemistry type in the display to NiMH.
Wait and see. But, hang-around just to make sure the charger isn't really broken.
