Well, since http://internal.bio3.pt/bio3cms/Data/Sites/1/skins/dcarter-sq2/csshandler.ashx?skin=dcarter-sq2&config=style.config&add= still results in 404 its clear that .ashx is still not configured correctly.
aspnetregiis is the tool for configuring .NET in IIS so that is the next thing I would try. Before using it you should google it and read up on using it so you understand what it does and how to use it. I think getting it fixed this way will be the best solution though there is one possible workaround you could try.
You can create a text file named csshandler.ashx in your skin folder and put this in it:
<%@ WebHandler Language="C#" Inherits="mojoPortal.Web.UI.CssHandler" %>
That will create a physical file to get past the 404 and hopefully invoke the handler. But long term you still will have other bugs come up if you don't really fix the IIS/ASP.NET configuration.
Hope it helps,
Joe