Thing is it's tough to compare when you say you heard them in different box, different amp, and different vehicle probably. You could swap all the audio gear from one vehicle to the next and it will sound different that's just the way it goes.

If JL asks for 1.25cu^ft and you have 1 cube that's not terrible, shouldn't be the main problem causing the poor performance. What deck do you have feeding the amp? I'm assuming you've got it and the amps crossovers/gains properly setup?