Thanks a lot for your comments and your additional research.
It was great that you confirmed that the language of the entry after the import should be Spanish as this was my default language.
I have tried again and now it worked fine. The EADS3 entry was imported as without errors and is stored as Spanish. I don't really know why it did not work the first time.
Even if EADS3 is not officially supported it seems that the differences are not so big as to prevent the import and the data looks fine.
I realise that importing EADS3 might not work in all cases but for the entries I have, it works a treat.
I wanted to mention also that I did not have any issues with the accents or the special characters in Spanish. From my side the file seems to be correct UTF-8. I imported it straight from my downloads folder without editing it in my computer.
I am really pleased with Atom 2. I am only wondering why I did not migrate earlier from ICA-Atom 1. :D