I've narrowed it down to the tracking generator, in both counts.
Buggy amplitude menu: Only happens when you are working with a normalized TG output. I would expect that when I normalize the TG, it should have a trace at 0 dBm (which I should be able to change in the normalize menu, and can). Then, everything should behave as normal. I should be able to move the reference trace (in the ampt menu) up or down. Up, for filters, down for amps. This doesn't work. If I turn the normalization back off (and accept the 4dB or uncertainty) it works as expected.
Noise floor/Dynamic range: When the tracking gen is running, the minimum value I can get out of the noise floor is -94dBm. Try it. Turn on the preamp, your narrowest RBW (10Hz in my case). Let it run for a bit with the power average. Now, clear the trace, turn off the TG, and do it again. At 1034 MHz I'm getting -140dBm. This is pretty disappointing. All I can really say, is that my distant rejection of my filter (which would block the image frequency) is better than 100dB. That's O.k., I guess, but not ideal. I'm thinking about using another signal generator to perform the measurement.
Ideas?