If it was about Bodoni font set, I'd like to say that we've found a problem and will include full solution in the upcoming update.
Reason of the problem was quite simple: source fonts had several copies of the same glyph (with the same name). It is not good.
Current solution is to convert to TTF and then convert these TTF files to OTF.
Our outline conversion algorithm is reversible (so it will not add errors to outlines). Hints will be regenerated, but it is also not a big problem since we use autohinting module licensed by Adobe.
4.0.2 update will be released right after NY.