Accordance 10.4.1 on WIndows 8.1 x64:
I think there is an issue with the text comparison option to ignore upper case (capitalization).
When I enable comparison for the GNT and GNT28-T the word ἀπεκρίθησαν / Ἀπεκρίθησαν in Joh 8:39 is still marked as different.
When I also enable the checkbox to ignore accents then it isn't highlighted.
Is there an issue with words having diacritics when using the ignore upper case checkbox?