So finally Microsoft have released the infrastructure update which once and for all fixes the problem with automatic workflows not working in Windows SharePoint Services 3.0.
More information: Description of the Infrastructure Update for Windows SharePoint Services 3.0: July 15, 2008
More information: Issues that are fixed in Windows SharePoint Services 3.0 by the Windows SharePoint Services 3.0 Infrastructure Update
More information: A declarative workflow that is configured to start automatically when e-mail enabled items are created does not start automatically after you install Windows SharePoint Services 3.0 Service Pack 1
Source: SharePoint blog