Tubes are made in batches, and while the JJ KT88's I've used in the past have been great, perhaps the batch that yours came from aren't as good? Hard to say as everyone hears differently too. I've used OS GE 6550A's, JJ KT88's, EH KT88's, Winged C 6550C's and they all sound good and are reliable, though the GE's cost a lot more. You can adjust the bias so it is biased a little colder and the amp will hold it together a bit longer before it starts to distort. You can also go to larger filter caps in the first two sections and use a solid state rectifier to tighten up the bass. It could be any number of things besides the tubes.
Greg