When battery charging the process is fairly inefficient so to put 3300mah into a pack of cells could mean the charger has to pump out 4500mah to reach that amount in the cells. All a charger measures is what it is putting out, not what is actually in the cells.
The cell rating legally has be a minimum capacity, so a pack of 3300mah cells should have at least 3300mah of capacity to be able to be sold. The worst 3300mah cells you can buy must have at least 3300mah in them, but many top spec packs of 3300mah cells would have a capacity of 4000mah or more which is why they were more expensive.
The 3300mah cells sounds more like the cells were out of balance, especially if left for some time. If one cell has more charge than the rest it will be fully charged first, but the voltage drop on that one cell when charged won't be noticed by the charger which only sees the rising voltage from all the other cells. To prevent this you have to discharge the cells first to equalise them out, or if you haven't got a cell discharger then trickle charging them all first will do much the same.
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