Now I have similar problems. The file name of the logo shows, but not the logotype itself … I have checked everywhere for any custom css but couldn´t find anything. Do you know what the error may be?
I managed to upload the logo on ftp after I got the file permissions correctly. But I can´t upload a new version of the logo directly via customizer, because the file name does not redirect in the code. It works perfect to upload the logo for Retina screen and sticky nav, but not the “regular” site logo.