The last line seems to indicate you had Application Manager open when you ran this. That's a no-no. Or maybe you weren't running as root?

Note that you can run apt-get update repeatedly and problems might fix themselves after a few tries.

When I have problems I can't fix I sometimes fix them running App Mgr instead of Fapman.

You could try disabling all your catalogs and see if the problem still exists, then add them back in a few at a time till you can figure out which catalog is causing the problem.

Those are the basic things I try. The last is to just wait and see if someone fixes any problem beyond my control.