How much better? Are we talking -42
dB vs. -40 dB, which is basically the same for all
practical purposes, or -22 dB vs. -20 dB, where
the 2 dB difference is more meaningful? The 40 dB
RL is hard to measure with certainty so a couple
dB is not too surprising.
could be that the length of the test cable is such
that the actual VSWR of the VNA Port 2 compared
to the WB load is different enough that the reflected
signal is significantly different.
have one available, take a Smith Chart program and
model your system, with cable length, assuming even
a 50+j0 ohm cable and then let the load be something
other than 50+j0 ohms and you can see how the measured
VSWR can be appreciaby different, especially if
you're measuring in the -30 or -40 dB realm.