Are the batteries Cadmium Suphide? Or are they NMH or Lithium? If they are Cadmium Sulphide, one of the problems is that this type of battery can develop a 'memory' and if partially discharged, then recharged again this makes the battery 'think' that it is fully charged, when in fact it isn't, hence the result you are getting. NMH (Nickel Metal Hydride) or Lithium do not suffer from memory effects.
This degeneration is additive and when the batteries are new the effect may not be noticeable, but as they age the effect eventually becomes more pronounced until they demonstrate the symptoms you describe.
There used to be 'dischargers' sold on the market to drain the battery periodically so returning them to their original state, but I am not sure if they are still available or indeed if the battery you describe has reached the end of it's life and cannot be recovered. I know that batteries used in our works radios many years ago had to be artificially discharged every 3 months or so and this kept them in good order for many years until the system was replaced.