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See bug 175756 to reproduce. If an installed site has a signed bundle with invalid signatures then the site is not available under Help->software updates>Manage Configuration My guess is that a verification exception is getting thrown and swallowed by update somewhere because there is no error messages when this occurs.
The Eclipse Update component is no longer under development, and no longer exists in the Eclipse Platform 4.x stream. If this problem still occurs in Eclipse Platform 4.2 or later, please enter a new bug report against Equinox p2.