I have the same problem, the Finnish characters åäö are being replaced by ?. The mail marked the encoding as UTF-8 (or rather Content-Type: text/plain; charset="UTF-8") in the header, but I suspect it's wrong, as when I forward the auto replied message in my client (Thunderbird) I get the ? replaced by the right characters.
I have ispconfig 3.0.3 (stable) on the server, and I saw a relevant entry in the bug tracker:
In case anybody knows the fix I'd be happy. Thanks!