DiffEngineX needs to insert blank rows into temporary copies made of the two Excel workbooks it compares in order to get similar regions to line up. Only when the cells have been aligned, is it possible to compare the formulae that reference them due to row insertion and deletion.
As such protected Excel worksheets cannot, by default, by compared by DiffEngineX.
Version 3.03 allows you to specify a password to unlock protected worksheets and thereby allow DiffEngineX to compare them.
This functionality can be found under Settings->Unprotect Worksheets.
If you are supplying command line arguments you should make use of the below.