I expect that there are three columns as an output, of which two should have the same value because the system does not differ in the x and the y direction. But I only get this output:
In Params.CrystalOrientation, EasySpin expects all three Euler angles for each orientation. So each row should have 3 values: phi, theta and chi. Since chi only affects the intensities, but not the resonance positions, you can use chi=0.
What is happening in your case is that EasySpin sees 3 rows (instead of 3 columns) and transposes the matrix to get the 3 columns for the 3 angles. As a consequence, you get something different from what you expected.