bad conetion
have you taken em off and clean em up
Your battery could have been in complete discharge and the current it was asking the charger for was to much for the charger and the overload protection was coming into operation to stop the charger from becoming overheated and damaged (the clicking you heard) so it gives the battery a little at a time to protect its self, once the battery was asking for what the charger could supply safely then it allows it to charge normally.I'll be surprised if your battery will give you good service from now on but you may have been lucky but don't hold your breath.Good Luck
It might be charged but Just no telling if it will now hold the charge.
when a battery gets completely drained like this, sulphates buiid up on the plates and wreck the battery.You can get small tablets from Halfords, I think they are called Bataids, these can remove the sulphates.If it's a sealed battery there's nought you can do
How long have you had the battery?