Darn, that’s too bad - perhaps it’s a contact issue, which is throwing off the voltage it’s reading from shorter cells?
With multi-chemistry chargers, I think they treat about <1.5V as NiMH, and >2.5V as Li-ion. So if it reads anything that falls in between, it would probably consider it a dead Li-ion and not be charged.

Perhaps you could try pressing down/inwards on the sliding bit of the slot while the 14500 is in there, to improve its contact with the rail and the cell?