In vba youwould use .Transparancy=.98 for example
In XML you would see something like this: (not the faces this site added those!)
<a:prstGeom prst="rect">
<a:avLst/>
</a:prstGeom>
<a:solidFill>
<a:srgbClr val="4F81BD">
<a:alpha val="98824"/>
</a:srgbClr>
</a:solidFill>
The alpha val represents the transparancy. There isn't that much that was possible in 2003 that cannot be done in 2007/10 using vba. There are things that can only be done in XML but largely they were impossible in 2003.
If it comes to it get in touch direct and once I've seen the problem I'll tell you if we can do it. We are pretty reasonable!
You can find my email on the contact page of
www.pptalchemy.co.uk