Hi Sven,
in most cases it's becuase chosen font doesn't support your language. As you know (or not yet) some fonts have only Latin, and you need full Latin-Extended. I have the same missing: ą, ł, ż, ś, ź, ż - with some fonts. So you're not alone ;]
Yes, sometimes problem is different, for example, if text was copy-paste using wrong coding in orginal text file.
You have to check if you have the same issue in Article, Module, and Page (SPPB) and compare results. Use the same text for each test. Copy from trusted document (text file), not current website.