When creating an Excel 2003 document using the OM, the SaveAs dialog is displayed with the document type of the template (.xlt) instead of the default type (.xls).
If I create the document from the document library ListViewWebPart toolbar, selecting my custom Content Type, the SaveAs works as it always does defaulting to the .xls file extension.
Under the circumstances at the client I am working for, I cannot try this with Excel 2007, but I suspect it is an Excel issue rather than WSS 3.0. Unfortunately, unlike a number of other warts in Excel, I cannot patch around this with VBA code in the template. When the problem occurs, clicking Tools > Options > Transition tab shows me that the default document type on Save is the default of MS Office Excel Document, or .xls that is.