Is the pump at the top moving? If not when it should be, first check to see that it is connected securely to the incubator port. Also check to make sure the humidity level is set correctly on the incubator. If the connection is secure, call Brinsea in the morning for help.
I keep my pump on a plastic container next to the incubator. It is not above the incubator, though I have thought about doing that so the pump doesn't have to work so hard. Also, the longer the tubing, the harder the pump has to work to push the water. You can try cutting the tubing shorter, if that is possible. A few air bubbles in the tubing won't hurt, but if you are seeing a lot of bubbles, you may have a pinhole leak in the tubing somewhere.