Akismet was the only other plugin enabled with wp-Typo, so conflicts there shouldn't be an issue. Funnily, I'm using Kimili Flash Embed in the other, working installation, and haven't come across any issues there, although this might be more due to the little use I have for Flash.
My hunch is that it still has to do with encodings, because the working setup's server defaults to UTF-8 while the non-working one's ISO-8859-15 has to be overridden with a "AddDefaultCharset UTF-8" in .htaccess. But after this, the headers and everything else seems to work as if the setup truly was UTF-8, so I can't see which component still might think it's not.
Anyway, the site has been released now, without wp-Typography at least for the time being. Feel free to poke the headers or anything you like with the site at http://www.osmy.fi/ --- though it's probably tough to navigate, unless you know Finnish. :)