... NOS power tubes seem to make the tremolo really happy, but new JJs make it weak (the intensity at '10' with JJs is similar to intensity at '4' or so with the original tubes). Is this because JJs are different enough ... that they bias differently and mess up the trem? ...
You know the answer must be "Yes" because the trem is responding differently.
However, this may not be a fundamental difference in the tubes, as much as it is the natural variance in how individual tubes of a given type bias up.
You probably bias by measuring current. If the transconductance (Gm) of two tubes is greatly different (expressed by Europeans as mA/V), each will need a different bias voltage to idle at the same current. If Gm is very, very different then the bias voltage will be very, very different.
I'm also guessing you didn't measure the bias voltage along with the idle current when biasing each set of tubes. Go back and check that while biasing each pair to the same idle current. My
guess is that a different (and larger) bias voltage is needed for the JJ's you have, and a bigger bias voltage makes the fixed trem output seem less effective.
If the RCA's bias up with less bias voltage needed, then the trem signal looks bigger compared to that bias when using these tubes, and thereby makes the trem seem to have more depth.
Maybe something else is going on, but largely the same thing occurs with 6L6's vs 6V6's, in that 6L6's generally use a larger bias voltage for an acceptable bias in the same amp, and result in the trem seeming weaker.