Hi,
from what you have said it appears that the pack has dropped below the lower level of charge that the charger can detect automatically. ( presuming the pack is not prehistoric and abused )
If you set the charger to a smaller battery pack size ie for 6 volt pack it is normally set to 5 cells, you should set it to 4 cells and charge it as normal
BUT ONLY FOR A SHORT PERIOD OF TIME SAY 5 MINS.
Then stop the charge and re set to the correct cell pack size, this will overide the auto cell detect on the charger and should bring the pack up to below its lower level the charger will now detect this and should charge as normal.
When charged re-cycle the pack a few charge and discharge times to ensure that the pack is in good condition.
This should sort the pack out, It has worked for me , and I was advised to do this by Ian when I had the prob and everything is ok.
Just try and keep the packs charged and don't let them drop too low on storage.
Regards Sub.