I'm having the same issue with 32-bit Windows Server 2008. My 3 Server 2008 32-bit boxes show up and all say the updates doesn't apply to your system. The conficker report always lists my Server 2008 32-bit boxes. According to the Microsoft Article, the fix applies to those with the server core installation.
*Windows Server 2008 server core installation affected. For supported editions of Windows Server 2008, this update applies, with the same severity rating, whether or not Windows Server 2008 was installed using the Server Core installation option. For more information on this installation option, see Server Core. Note that the Server Core installation option does not apply to certain editions of Windows Server 2008; see Compare Server Core Installation Options.
It seems like this is a false positive. However, the Server 2008 R2 boxes we have don't show up in the conficker list. Hope this helps.
