It is probably air trapped somewhere that is slowly getting pulled through the system. It should eventually work it's way to the top of the boiler and escape. Try quickly closing and opening the valve on the return at the boiler a few times and see if it brings larger amounts of air through the system. You may be able to quickly get it out this way.
Where do you have the pump mounted? If in the house, I would make sure there isn't a leak before it. If it is bad enough it could be pulling air in. To test it, you could close the valves at the boiler and pressurize the system with domestic water to full pressure and check for leaks.