Unfortunately I don’t believe the issue has anything to do with 32 vs 64. There’s something else that SCCM is doing with the target WSUS server, that I believe is the source of this problem. In SCCM 2007, I believe that SCCM essentially takes over the WSUS server that it’s linked to, and this is the cause for WUA searches returning no results. For example, if you look at HKLMSOFTWAREPoliciesMicrosoftWindowsWindowsUpdate on a machine that you’re trying to patch with BatchPatch, you’ll see the WUServer and WUStatusServer registry entries, which will be populated with the update server that SCCM is configured to use. If you have a separate WSUS server that is not linked to SCCM, you can manually change these reg keys to point to the unlinked WSUS server, and then you’ll see that BatchPatch finds updates to download/install.
-Doug