Sounds like the amp hour (AH) rating for the charger is way higher than the AH rating of the battery.

On the charger spec plate you should have an amp hour or AH rating. On the battery, there should be a data sticker or a stamp in the side with a number that looks like this: 18-85-17

We know your charger is 36v so the first group will definitely start with an 18-x-x. We need to fill in the last two blanks.
(the battery number is also stamped into the intercell connector closest to the positive cable. Don't try to look if you don't have experience as you can potentially short out the battery and can get hurt, burned, acid thrown on you, etc... be careful!)

It's simple to figure out though. Using the example above:
18-85-17
18= number of cells X 2 volts per cell = 36 volt battery.
85= Amp hours per positive plate
17= number of plates per cell (each cell has one extra negative plate)

To get the total AH of the battery, multiply the AH per positive plate by the number or positive plates in the cell. So in our example:
17 ÷ 2 - 1 = 8 positive plates.
85 X 8 = 680 amp hour battery

So if you used a 1200AH charger on our example battery it would fry it.

EDIT: I believe your charger is a 680AH charger based on the 680 in the model number.