I see the problem now. We want things to be horizontally centered, but they aren't.
First of all the problem is not related to IE6. We get the same rendering in Firefox as well.
I can assure you that many coders are crumbling their toes out there when they take a look at the code which appears to be generated by software.
Anyway I guess we just want the page up running quickly, so let's exercise doing some patching.
1. Centering the page.
We must properly center the page, which in our case is achieved by replacing the body selector portion with this:
margin: 0 auto;
2. Correct position properties for child elements of the 'body'
Now, since the 'body' element takes care of the left margin, we must also correct child element properties: (here the original values of the 'left' properties have been subtracted with the same value)
<div id="Layer1" style="position: absolute; width: 800px; height: 600px; z-index: 1; left: 0px">
<div id="Layer2" style="position: absolute; width: 220px; height: 157px; z-index: 2; left: 139px; top: 77px;">
<!-- the 2nd Layer5 !!! -->
<div id="Layer5" style="position: absolute; width: 319px; height: 28px; z-index: 5; left: 108px; top: 42px;">
<div id="Layer4" style="position: absolute; width: 909px; height: 83px; z-index: 4; left: 0px; top: 460px;">
<div id="Layer3" style="position: absolute; width: 213px; height: 141px; z-index: 3; left: 139px; top: 296px;">
3. We have two div's both having id="Layer5" which is not allowed. The first one is nested within div 'Layer1' and is not the one I am refering to above. We should leave the style attribute as it is for this one. Not that browsers care much, but still, we'd better rename it to e.g. Layer6.
Try steps 1-3 and let's see what the effect is.