It isn't unusual to hear what you describe considering how much gain is needed to boost the minuscule output of phono cartridges to line level for the subsequent stages. The gain of the stage can be reduced if you want to get inside and do some modifications; but if it doesn't bother you, I'd forget about it. From what you describe, the signal to noise ratio is sufficiently high to not be an issue when the music is playing. That's the only thing which matters.
It seems that you are simply experiencing gain differences among the different tubes. Although they are all supposed to meet the same criteria, in actual practice there can be fairly large variations. So, if your JJs are running on the high side, and the EHs on the low side the difference can be striking. You can verify that it's not a socket issue by simply rocking the tubes slightly while listening (with no music playing). You will know quickly if there's a problem.