It looks like the transformation from MJ2000Eq with Origin Mars and the TODEq with Origin Mars is wrong. Use the following inputs for the initial orbit of a S/C:
Epoch: TTGregorian 1 Jan 2000 12:00:00
Coordinate System: TODEq with Origin Mars
And then compare the coordinate system related angles RAAN and INC in MJ2000Eq and TODeq with Origin Mars, e.g. with a Report file. The values in these two coordinate systems are almost identical. At that epoch this is only true for the Earth, but on Mars the differences between TODeq and MJ2000Eq is much bigger and the orientation of Mars at the J2000 epoch is for sure not identical to the orientation of Earth.