Common causes:

• There are discrepancies for options used in the GUI and command line
• Different objects are selected in the GUI/specified on the command line

Ultimately we need to make sure we are comparing the same objects with the same options.

One pitfall when using the command line is if you don't explicitly set any options, the defaults are used; however if you want to use default options with additional options, you must specify the default argument and the additional options. For example:

/Options:Default,CaseSensitiveObjectDefinition,IgnoreComments

If you use compare project file on the command line, you need to make sure all wanted objects are selected before you save the project file. If you need to add or remove objects for comparison, you need to update it from the GUI, re-save the project file and use the updated project file from the command line.