shaft encoder and counter

Hi all,
ther are some varius counters, that they had not any similar parameters, counters connected to shaftencoders. when we connect our counter to shaftencoder, we count the numbers, so when we connect original counter to shaft encoder, we count previous number with 1% error. i can not find my problem and it is very important to me. if you know, guide me please.

What type of shaft encoder are you using? What are you using for a counter?

there are several types of them and we don't have any specific .
also this problem is the same for counter. for your knowledge I should say
the counter is gas pump for petrolium.

Do the shaft encoders start and stop smoothly or do they rock back and forth during acceleration and deceleration?