Compatibility with themes that put all javascript at the bottom

Check your javascript errors. You may find that because Blueprint puts all the javascript at the bottom of the file, inline "Drupal.extend" calls will be broken.

Right that is likely the cause. I think then the issue is with how FCKEditor defines it JS since if it is setup correctly it should still work.

I suggest moving this issue over there...

I will put this at the todo list

5.x fixed in CVS.

Fixed in 6--1 and 6--2 as well.

I'm not sure about 6--2 though, in 5--2 and 6--1 I used:
if (Drupal.jsEnabled) {$(document).ready(function() {'. $js .'});}
but in 6--2 I had to remove document.ready call to start FCKeditor. It definitely has something to do with the new loading method of FCKeditor (Drupal.behaviors)... so please correct it Jorrit, if you think it should be done in a different way.

I use last version of Drupal and FCK. When I move
print $scripts;
just before tag, how is written here:
http://craigsworks.com/projects/qtip/docs/#installation

It is highly recommended that all JavaScript includes like the one above be placed after all your content at the footer of the page, just before the end tag. This ensures that all content is loaded before manipulation of the DOM occurs.

FCKeditor never render again. When I copy it back to FCKeditor start works again (so I leave it there for the present).
So this issue is not absolutely fixed IMHO.

I found ** solution here **
http://wimleers.com/article/improving-drupals-page-loading-performance#r...
It should be

      ...
      <?php print $scripts ?>
      <?php print $closure ?>
   </body>
</html>

..and FCK works.

This was also mentioned at http://drupal.fckeditor.net/troubleshooting#1.