Wim,
I still noticed a small anomaly. In the Modulus diagram, now having the correct phase, the cursor below the image still gives the phase of the bode diagram.
Then I have a few suggestions concerning noise fighting in noisy pictures, although I have no idea whether or in what way noise fighting is already part of your software Tool.
1) the most simple step would be when testing up to a frequency A, to limit BW of both channels to a BW of 5A or something like that.
The scope's BW in my case of 100mHz, has a noise of 100uV.
When measuring up to 100kHz, BW could be limited to 500kHz, already giving a possible noise reduction of 23dB.
2) Since it is possible to "overlay" several measurements in your program, it would help to reduce noise when they could be averaged.
Kindest regards,
Hans