You should have stated whether the batteries are nicad or nimh.
The charger should "work", ie charge the batteries, but the automatic voltage trip points are set for a lead acid wet cell.
The high voltage fast rate charge should cease (peak at) at 7.1 volts, and switch to maintain the batteries at 6.1V or 6.6V (using the 6V setting).
The wet cell voltage is a nominal 2.1V/cell fully charged (rested). During charge they can reach 2.4V/cell.
A nicad cell is 1.3V charged (rested) During charge they can reach 1.4V. So, an automatic charger intended for a wet cell battery won't be automatic for a Nicad.
Good nicad chargers monitor the battery charge voltage for delta peak. When fully charged, the battery voltage drops about 10mV/cell, and the cells start to heat up. Good nicad chargers notice this and reduce the charge current.
What is unknown is if your charger is a constant current type or constant voltage type. However, it would seem that either would overcharge your nicad or nimh pack.
Your pack discharge rate is 3000mah or 3 amps (this is your C rating). If you discharge at that rate you will notice battery heating (not good for batteries, recharge after cooling).
You can charge the batteries at that rate, too. This would be the C/1 rate or 3 amps. To avoid heating the pack, it is best to charge at C/10 (0.3 amps). If you wish to maintain the battery at full charge the C/50 is desired and will keep the battery at full charge. At a two amp rate you can expect the pack to heat up to unacceptable levels before reaching peak charge
If your charger is a constant current type, it will attempt to charge the battery at 2 amp. You can monitor the battery for heat and charge voltage and disconnect when it is full. But, don't expect it to be automatic for Nicad cells.