The only two other causes I can think of are gas saturation issues. With high intensity lighting and alot of algae or coral growth the water saturates with oxygen and this is identified by a problem worsening as the daylight hours continue and being almost non existant in the morning. The solution in this case is to reduce the photoperiod or remove some algaes. A reverse daylight refugia could add to the problem because there is constant oxygen production.
The other possibility is an excessive KH or dissolved CO2 from a calcium reactor is skewing the carbonic equilibrium and the gas is being removed in the pumps partial vacuum. Such a problem is constant until the KH is reduced or the excess CO2 is relieved.
You might also give it some time after cleaning, it can take a few days to remove all the bubbles from inside the magnet well, assembling the pump under water could alleviate this cause.