Using Atahualpa 3.6.7 on testsite http://hybrid007.ic.cz (it is in Czech) - I want to use external javascript file for displaying dates and birthdays. I inserted this code to ATO - Add HTML/ CSS inserts/ HTML Inserts: Header:

<div id="svatek">
<script src="http://hybrid007.ic.cz/wp-content/themes/atahualpa367/js/svatek2.js" type="text/javascript" language="JavaScript"> </script>
</div>

Script is showing (in the right corner is text "Dnes je...") - but as you can see - Czech characters (as "á", "č" or "ř") are not displaying - I tried setting charset as utf-8 in the header.php and in other places, but none of them worked...
Really appreciate any help!

It looks like you don't have the 3.6.7 PATCHES applied, start by applying them all. Here are the links.

• PATCH 367-01: Odd effects when 'CSS: Compress' = 'Yes'
• PATCH 367-02 is incorporated in PATCH 367-04
• PATCH 367-03: PHP errors when adding widget areas in index.php
• PATCH 367-04: Hovering over a Post/Page title only shows "Permanent Link to"
• PATCH 367-05: Site Title appended after the 'WordPress SEO by Yoast' title

this might also help http://www.meanfreepath.com/support/..._charsets.html

Sorry and thanks juggledad! I didn't realized it! But even when patches were applied, issue remained.
Finally I got it - beginners mistake: when you want to save file from notepad as js file, remember to save it as UTF-8 (not as ANSI) and as a file-type: "all files" (not txt)!
So server and theme settings was alright, it was the js-file which caused this issue! Thanks juggledad again for your time!