Dragan,
Thank you for clarifying what you did on your tests. I took a look at the .s2p file that you posted and see that you get the same large S21 phase shift that I got in my tests. I posted my plot of your S21 data below. For a tiny SMD resistor like the one you used the phase shift should be minimal (at least on the lower frequencies.). The S21 magnitude loss is very close to what it should be for a 10K resistor but that phase shift will give a lower R value and indicate reactance that isn't there if I understand this correctly. Do you agree?
I also did a conversion from serial to parallel impedance and your S11 measurement was surprising close to 10K ohms. For a VNA designed for 50 ohm system impedance this was very good. Plot attached.
Roger