If the battery is flat (1V per cell) and you charge at the 1C rate (ie 3300mA for 3300mAh) then it will take ~1 hour + a bit for the efficency loss & some types of chargers turn off every minuite or so to check the battery voltage). If you want your batteries to last dont charge more than this. Trickle Charge is usually 1/10C (ie 330mA for 3300mAh) and can be left on perminantly but most recommend 14 hours). Chargers that display capacity while charging is only an estimate but is usually pritty good. To find out the true capacity you need to fully charge and then discharge to 1V per cell. Note battery capacity is usually measured at a 1/10C discharge rate (depends on manufacture) so discahring at 1C rate will reduce the capacity displayed on the charger but NiMh are quite good at that rate so wont affect them much, Pb ones are the worst.

In any case if you discharge at 1C and it takes less than 50 mins(1 hour for 3300mAh) something is wrong, at 1/10C it should not take less than 8 hours (10 hours for 3300mAh). If its not your battereis then its your charger but it sounds like one of them is wrong if the charger is setup correctly.