I used up to version 2.39j and everything was fine:
FLAC tags with text with accents like è, ê, é were displayed properly in the export HTML file.
After installing V2.40 in the HTML files these letters are simply dropped: in IE a small box is visible, viewing the source no letter at all is visible. As a consequence no links with names containing these accents (tracknames) works.
In Mp3tag itself the accents are visible, just not in the export file.
Downgraded to 2.39j and it worked again.
Using WinXP localized (Dutch), tags in UTF-8, charset in HTML is also UTF-8.
Nothing else changed, just the version of Mp3tag.