You are charging the battery at too low of a rate.

You are safe up to 1C w/o problems, so your 3400mAh pack would accept a 3.4 amp charge current.

Cut that in half and you are still at 1.7 amps, so charge at 1.5 to 2 amps if you cannot hit 1.7.

With the 900mAh batteries at 350mA you are closer to their .5C current... which is why they work for you.