I just tried what you described and confirmed that (at least on my OSX machine) ADE fails to load files containing the ByteOrderMark.
Here's what I did:
I created a simple html containing a paragraph with bold text and added an external stylesheet which resets the font-weight of the bold element to normal.
When I create the book with those files in the normal UTF-8 (or ascii) encoding everything's fine. But if I change the encoding of the stylesheet to UTF-8 with BOM the bold element is displayed bold again, meaning that the css file has not been loaded. Whats even more curious: changing the encoding of all of the other files to contain the BOM as well doesn't disturb ADE - even for the mimetype file. So stylesheets are the only one affected...
What does that mean in your case? You probably have either presentational elements in your html markup (b, hx, unclosed hx, ...) or you have a css rule somewhere that declares your global text as bold which is then overridden back to normal by the stylesheet with the BOM - which isn't loaded due to its BOM, so the text remains bold.
Don't use the BOM and you're fine.