This might be somewhat related. I see jumbled diacritics in PDF bookmark headings after conversions.
Uninstalled 6.18.1, reinstalled 6.17, then diacritics in PDF bookmarks display correctly after conversions.
I usually prefer to do PDF conversions with 3.48 Portable, because
of this issue, so I wonder if it would be possible to bundle Calibre with both PDF engines (Podofo and the original one from versions < 3.48)