It seems to me this is a problem with your configuration/ environment. See the CKEditor demo (latest CKEditor release with default settings) with the same source code that you pasted:
<span style="color:#ff0000;"><span style="background-color:#ffff00;">His cook put the worms on the barby.</span></span>
If you insert this in Source view, switch to WYSIWYG and back, the issue that you described does not occur.
Re: delimited quotes
If you insert this in Source view, switch to WYSIWYG and back, the issue that you described does not occur.
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Re: delimited quotes
I assumed it was a configuration issue but unfortunately the Demo page doesn't reveal the editor's configuration.
Here's my config... what have I missed.
<form method="post" action="savetext.php">
<p>
My Editor:<br />
<textarea name="editor1"><?php $top=file_get_contents("notices.txt"); echo "$top" ; ?></textarea>
<script type="text/javascript">
CKEDITOR.replace( 'editor1',
{
toolbar : [ ['Format','FontSize','Bold','Italic','Underline','TextColor','BGColor','Cut','Copy','Paste','PasteText','JustifyLeft'
,'JustifyRight','JustifyCenter','JustifyBlock','HorizontalRule','NumberedList','BulletedList','SpellChecker','Table'
,'Print','Link','-','Source','About']]
}
);
</script>
</p>
<p>
<input type="submit" value="Send"/>
</p>
</form>