Did you replace all the tubes or just the power tubes? If you replaced all of them, maybe try your old preamp tubes with the new JJ power tubes.
Clanky would be a good description of how JJ tubes sound to me.
Anytime you make a change like that, it is going to sound different. Give your ears a chance to adjust. Also try to adjust your tone either at the guitar, or with the treble mid bass knobs on the amp.
The fact that it sounds different means you did probably prove the issue was with the tubes. Unless it still sounds the same? But it sounds like it changed the sound, but to another sound you don't like.
I try to stick with tubes I like, not so much that one is better or worse, but more it will have a sound that I am used to, and found pleasant before.
Maybe the tubes will mellow out after few hours use? I know Emminence speakers need some break in. Perhaps JJ tubes need it also?
Maybe you are just hearing the limitations of the Blues Jr amp? It's not a great sounding amp.
When I first got my Egnater Rebel 30 I really had a hard time with it. It was so forward and in my face. Not all dark and subdued like my Fender Princeton. The old fender amps had so much negative feedback to reduce the distortion levels, if really cut back on the dynamics and the frequency response. I had just spent $900 on an amp I didn't like? But I learned I needed to roll off the tone knob on the guitar just a bit. I also needed time for my ear to adapt to the new sound. I noticed there was a lot more of the guitar there with the rebel 30. I learned how much reverb to add in, which was part of it too. And I also learned that if I played subdued, then the sound was also softer. But when I used more attack on the pick, the amp brought it right through to my ears. Not something you are going to get a Princeton to be able to do, no matter how hard you bang on it.
So give it some time, and see if the tubes mellow out, or you find a way to adjust the tone to make it sound better, or maybe your ears just adapt?
My favorite is TungSol power tubes, with an ElectroHarmonix phase inverter tube. I don't know why, but it seems to work. The most important tube after the power tubes is the V1 preamp tube. I really highly recommend the Tube Store Select series 7025.