You have a point. Even without BOM the program still recognize that the first block is in utf8. How could he don't think the same of the rest of the file?

That's just it, Perl will threat the whole file as utf-8. It seems you are likely corrupting the file during upload. If you post the relevant code you are using to handle the upload, probably some monks can either see what's wrong with it or give a alternate approach for uploading which avoids the problem.