My guess is that your hydraulic lines are long, high capacity, metal tubing that is driving a relatively small capacity actuator.
It could be countered with a small hydraulic accumulator or by replacing metal lines with rubber hydraulic hose that can act as an accumulator because they are more elastic than metal lines.
A much thinner line to the actuator could also resolve the problem because the ratio of the volumes is important.
On a double acting system, the contraction effect could also be countered with a pilot operated lock valve on the actuator.
It is possible that the system worked when originally commissioned because some air was trapped in the line. Now that it has been bled, there is no accumulator effect. Can the air bubble situation be restored safely to test the hypothesis?