When Li-Ion batteries are discharged to a too low voltage (below 2,75 V/cell, in this case 13,75V) the charger will assume that the battery is damaged, and will not charge the battery. First measure the battery voltage with a volt meter, if the voltage is significally below the 13 V the battery are no good. If you have a reading of lets say around 10 V, you can raise the voltage shortly on the battery, by jumping it with a fully charged battery. Connect the "-" poles on each battery. After this, shortly connect the "+" poles, for no more than 5 seconds,disconnect the wires and immediatly put the battery in question in the charger. If it starts charging, every thing if fine. If not, try the process again, you might wanna recheck the voltage if it rises.
Please be aware, that over discharging Li-Ion batteries, will lead to damage of the Li-Ion cells, which results in loss in capacity, therefore, if you are not to use your Li-Ion tools for a while, make sure the batteries are fully charged.
Hope you guys could have sucess with the above