The subsetting feature is very useful. It will frequently reduce the space used for fonts by almost 90%. But on occasion it would appear to lose characters from the font. The examples below are with the small cap characters from LinBiolinum_RB. The first image is how the text appears in ADE without subsetting.
If I subset the font the heading looks like this:
With Calibre the result is similar except that the fallback font makes the error more obvious:
Is this a problem with Calibre? Is it an user error? Or what?