There is a bug we highlighted in the mailinglist some months ago and which doesn't seem to be in the buglist nor doesn't seem to be solved either. It was a bug with the midi2ly app which doesn't use the --key information to fetch the midi file and put "a is" instead of a "b es" in a F major piece : --key=-1.
(I wonder if this feature was working in a previous version of lilypond like the 2.8.6 or so)