As I understand the OP, the device is designed to use a Lithium Polymer cell which has been replaced by NiMH cells. The two chemistries have entirely different requirements for charging. A LiPo only charger cannot understand how to charge NiMH as it is not equipped to monitor for slight drop in peak voltage when the cells are fully charged. The same goes the other way, NiMH/NiCad only chargers cannot charge LiPo cells as they require a very different CC/CV algorithm where charging is halted when the cell drops to only accept 1/10th of the original charge current in the CC portion, when in the CV portion. I suspect the charger control is detecting what it sees as an out of spec battery, perhaps the voltage is simply too low in the discharged NiMH pack, but no matter, the chip will not know when to shut down charging as the current acceptance would not drop as it does in a LiPo. The only hope would be for a timer to shut things down, but I have no idea of what's in the device mentioned.
Moral, use a LiPo charger to charge LiPo's. Use a NiMH charger to charge NiMH, and don't mix the two up.
Regards
Christian