I was thinking that perhaps your brief running of the genset or engine was too short and not be enough to charge the batteries. This would show up even right after you shut the engine down if batteries showed significantly
lower than before you started up, however BFlinn181
is right, for more precise reading wait about 4+ hrs before taking the second measurement.
's post has the definitive test. You can get an idea of state of charge from this reference. Measuring State-of-charge - Battery University