Well, there can be lots of possible reasons... They are both direct conversion receivers, with local oscillator going from low vhf to high uhf band.
We can expect lost of silicium bugs here : power level of the local oscillators frequency dependant, quadrature mismatch, mixers with conversion loss not constant etc. etc.
honestly it is not easy to know; I guess this also depends on the part itself. My experience show that from one E4000 to another, the preamps can completely behave differently. On some units, when manually set to more than 17db, it works as an attenuator :-( the power level received decreases....
For me the most interesting plots were the "no antenna" ones, showing the LO leakage ;-) If I understood clearly your plots, you have at some places high power ghosts. Maybe you are close to powerful transmitters, but this is more probably a LO to RF isolation problem: the receiver receives himself...
I usually play with the E4000, but I am waiting for some 820T to try.