Hi Umberto,
Yes, you should remove the BOM mark from the file and it should work - totara_sync uses the standard PHP library functions for importing the CSV file and does support UTF-8 so most likely the BOM is the issue here.
Regarding your issue running totara sync from the command line - it may be that your data directory is owned by the web server user and the user running the command at the command line doesn't have write access but the web server does.
Normally I'd run it with a command like this:
sudo -u www-data php -f run_cron.php
which runs it as the "web server" user.
Simon