This seems to be a problem with missing assembly reference. JustDecompile needs all missing references to be resolved in order to produce the most accurate output. The GUI of JustDecompile have mechanisms, that ask the user for the path to certain assembly when it needs it, as opposite to the command line interface, which does not have any of those. Have you resolved some assembly references when you were using the GUI of JustDecompile?
By default JustDecompile will look in the same folder as the exe/dll for all of its references. If you put all references, which you resolved in the UI, in the folder of the assembly then you should get the same result.
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