I had a similar problem with viewing the entire SCM history (Subversion in this case) when viewing the "Repositories" tab in the "Organizer" from Xcode 4.02, where I could only see revisions for the selected folder in the "History" panel, as well as revisions from the subcategory directories are not displayed.
To see the full story (that is, the visual equivalent of “svn log” in the project), you need to select either the root repository (purple icon) or the branch (yellow icons) for your project.
After selecting any of these icons, all revisions should now be displayed in the history panel, including changes to subdirectories that would otherwise not have been displayed if a working copy (blue icon) was selected in the left panel.
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