OK, it gets a little complicated. Fist add a z-index higher than any other z-index on your page to the fixed division(s). A z-index of 10 is usually fine:
Code:
<div style="position:fixed!important;position: absolute; top: 40%; left: 40%; width: 100px; height: 50px; background-color: #990000; border: 2px solid red;z-index:10;">
Next, create a container division within IE conditionals for all the other content on the page:
Code:
<!--[if gte IE 5.5]>
<div style="position:relative;width:100%;height:100%;overflow:auto;">
<![endif]-->
Have that follow all the fixed content and place its conditional </div> tag just before the </body> tag:
Code:
<!--[if gte IE 5.5]>
</div>
<![endif]-->
</body>
Now you can put normal absolutely positioned content (as well as regular content) within that division and it will behave as expected.
As far as where to put the the IE styles currently in the head, you can put them anywhere you like as long as they are parsed by the IE browser. They will never be used by any other browser anyway.
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