There are two methods of encrypting fonts:
1) Adobe
2) IDPF
epubcheck will only accept the second. Actual EPUB readers usually only accept the first. So calibre uses the first. IMO epubcheck is an unmitigated disaster. Do you want an epub file that passes epubcheck or one that is actually likely to work on actual epub readers?
Versions of calibre prior to 0.6.41 did not obfuscate fonts, so you wouldn't get the error with epubs produced by them. But including un-obfuscated fonts in a epub file is a copyright violation for most fonts, which is why updated versions of calibre obfuscate fonts.
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