As explained on the GSX manual, and so many times on the forum, GSX estimates the number of passengers by dividing the total station load by 220 lbs, which is the industry standard to estimate how much a passenger + luggage weights.
But this doesn't necessarily work with all plane configurations (full passengers, combi, etc.) or to whatever the 3rd party airplane you are using sets on its loading stations, and when.
In the latest version, we added a new control variable that 3rd party airplane developers can write to, to TELL GSX how many passengers they are assuming, so the two will be in sync. But it's a brand new addition, and requires changes in the airplane code to support it.
We contacted some popular developers (FS Labs, Aerosoft, TFDi, etc. ), explaining this feature, and they seem to be interested adding it to their products.