I think I found one "ugly" solution!
I made a script that change the LANG variable from utf8 (default in my system) to iso88591 that is used in Spain too.
export LANG='es_ES.iso88591' ; calibre
And now, the character input works fine (with same console errors), while I'm searching a real solution. The folders in window of "add books" still show that characters, but the input was the really annoying problem.