It is apparently related to the font. In flash albums the "Myriad Web Pro" is used and in HTML albums it is the Helvetica family.
The text I use for testing is "Fra Skiathos til Skopelos –aæaøaåaaÆaØaÅa"
If I changed the font in the styles.xml (flash album) to e.g. Arial, the text is shown correctly. If I put the text in a Word document or a Notepad and apply the "Myriad Web Pro" font, the text is shown correctly.
I have attached a 'clip' from a screenshot of the flash album.
I do not recall using flash albums with LR3. I will try to install it (LR3.6) on another PC.