You are both right. The pulsing is due to control software in the charger unit.
When the battery is on charge its apparent voltage becomes higher than when it is off charge. So "the higher voltage is confusing the charger", absolutely right but the charger is aware that it is being confused by the battery's apparent voltage.
The charger therefore turns off the charging for a few seconds to let the battery "relax", and then it measures the battery voltage while it is in the "relaxed" state and off charge.
If the "relaxed voltage" shows that the battery needs more charge then it delivers another charging pulse to the battery, and so on. This is all OK and perfectly normal.
You may find the pulse rate and pulse length (the so-called mark-step ratio) also varies according to the level of charge in the battery, in other words the charger gets bolder at certain times and whacks the energy in, and at other time it gets more cautious and delivers tiddly bits of energy.