yes, it takes some time for your breast to get accustomed to the new pump. and the right breastshield size is also important. of course, manual expression is the best (IMO), just second to the baby's suction and you can adjust to different angle of expression. but if you need to express milk very often, manual expression may hurt your tendons. too much repeated motion.
when i wanted to to increase milk production, i kept pumping every 3 hours. even after the breast is clear, i continue to pump lightly for 5-10mins, just to stimulate the breast more. see if that helps you.