I just exported a Mac Notes entry as a PDF to my encrypted Dropbox folder, but it was not encrypted (no .bc extension). I'm saving directly to the Dropbox encrypted folder, not through the Boxcryptor folder.
Another example: an exported JPEG file from the Photos app fails to get encrypted.
New and existing Microsoft Office files get encrypted properly when saved directly to the encrypted Dropbox folder.
Yes, Boxcryptor is running and logged into.