Illustrator Layer positions are off in AE5.5

Hello Kind Forum Geniuses,
I'm having trouble with after effects projects in CS5.5. The projects in question were originally created using CS4. Basically we have a number of Illustrator assets (also created with cs4) that were imported as compositions (without retaining layer size). When these projects are opened in CS5.5, the layers are all over the place. I've tried opening the illustrator files and saving as CS5, but that doesn't seem to work. The funny thing is that we aren't having problems with any illustrator files brought in as a comp retaining layer size.
Anyone hear of a fix for this issue?
Thanks,
Dennis
Mac OS X 10.7.3
2x2.4 GHz Quad-Core Intel Xeon
24 GB RAM

Thanks for the reply, Mylenium. I just tried saving the illustrator files down to CS3 with no success. We thought that maybe Adobe changed the way that they handled the "artboards" in Illustrator and that was the root of the issue, but we have no way of telling. I'm hoping there's a solution other than manually updating each layer in our projects (hundreds at this point!).

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Firefox on PC, and all Mac browsers do not correctly place
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Murray --- ICQ 71997575
Adobe Community Expert
(If you *MUST* email me, don't LAUGH when you do so!)
==================
http://www.dreamweavermx-templates.com
- Template Triage!
http://www.projectseven.com/go
- DW FAQs, Tutorials & Resources
http://www.dwfaq.com - DW FAQs,
Tutorials & Resources
http://www.macromedia.com/support/search/
- Macromedia (MM) Technotes
==================
"Anthony LeBaron" <[email protected]> wrote in message
news:[email protected]...
> Sorry Murray,
> Was not able to post file since it contains unreleased
financial data...
> Nowever, I have repaired the problem but I don't
understand the issue.
> Maybe you can explain.
>
> Each layer was a div tage with an absolute position.
> Within the div tag was a small text field.
> The first line was within a span tag with a specific css
style.
> The following lines were within a second span tag with
another css style.
>
> If the div tag was immediately followed by a <p>
(i.e., <div><p><span>...)
> the layer was positioned properly in all browsers, both
mac and pc.
> If the <p> was omitted, the layer would position
correctly in IE (pc) and
> in Dreamweaver preview. In other browsers and on the
Mac, it would display
> higher than specified.
>
> This doesn't seem to make sense to me. Does it to you?
>
> Here is the code used within the div tag.
>
> <div id="Emp06">
> <p>
> <span class="Name">Lorem Ipsum</span><br
/>
> <span class="Title">
> tile line 1<br />,
> title line 2</span>
> </div>
>
>
> "Murray *ACE*" <[email protected]>
wrote in message
> news:[email protected]...
>> Would need to see your HTML too. Can you post a link
to the page?
>>
>> --
>> Murray --- ICQ 71997575
>> Adobe Community Expert
>> (If you *MUST* email me, don't LAUGH when you do
so!)
>> ==================
>>
http://www.dreamweavermx-templates.com
- Template Triage!
>>
http://www.projectseven.com/go
- DW FAQs, Tutorials & Resources
>>
http://www.dwfaq.com - DW FAQs,
Tutorials & Resources
>>
http://www.macromedia.com/support/search/
- Macromedia (MM) Technotes
>> ==================
>>
>>
>> "Anthony LeBaron" <[email protected]> wrote in
message
>> news:[email protected]...
>>> Having problems with layer position. Dreamweaver
preview is correct, as
>>> is display in Internet Explorer.PC.
>>> Firefox on PC, and all Mac browsers do not
correctly place top value
>>> (left value is correct)
>>> Any ideas? All layer attributes are in css.
Emp01 below is correctly
>>> placed. Emp07 is not. All layers given unique
Z-index
>>>
>>> #Emp01 {
>>> position:absolute;
>>> left:183px;
>>> top:275px;
>>> width:180px;
>>> height:42px;
>>> z-index:1;
>>> visibility: hidden;
>>> }
>>>
>>> #Emp07 {
>>> position:absolute;
>>> left:600px;
>>> top:265px;
>>> width:175px;
>>> height:61px;
>>> z-index:7;
>>> visibility: hidden;
>>> }
>>>
>>
>>
>
>

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But when we are running the application these changes are not reflecting, do need to restart the server to get the model layer changes reflected.
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