If the battery is quite flat it will draw a lot of current. If your charger is only a small charger (at 5 amps I would think it is a small one) then it won't be able to supply the battery with loads of power and will trip out from time to time to allow itself to cool down. Once it's cooled off it will charge again before tripping it's thermal over load again. this is normal and all battery chargers have the facility. you're just asking too much of it.

A 5 amp charger will charge more (probably double so 10 amps) but they are only rated at a continuous 5 amps before triping thermal overload protection.