Consider the following scenario. In a Windows SharePoint Services 3.0 site, you create multiple custom content types, and you add these custom content types to a document library. Then, you change the document library setting to use the custom content type as the content type for the document library. After you make the change, you can select the custom content type from the New menu, upload the file, and fill in the selected custom content type fields. In this scenario, if you upload the same file that you chose previously, the custom content type that you select from the New menu is not used. Instead, the built-in content type of "Document" is used.
To resolve this issue, apply the following update:
975002 Description of the Windows SharePoint Services 3.0 Cumulative Update Server Hotfix Package (Sts-x-none.msp): October 27, 2009
This update can only resolve the problem for newly added documents. Existing documents will not change. Therefore, you must set the content type back to "Dublin Core Columns" for existing documents.
Microsoft has confirmed that this is a problem in the Microsoft products that are listed in the "Applies to" section.