I think this is related to phased updates. I realized the same behavior today and running "update-manager --debug" on terminal showed the reason:
DEBUG:AptClient.DebconfProxy:debconf socket: /tmp/aptdaemon-mv4t9int/debconf.socket DEBUG:root:debconf.start() DEBUG:root:debconf.stop() INFO:root:holding back phased update compiz (0 < 26) INFO:root:holding back phased update compiz-core (0 < 26) INFO:root:holding back phased update compiz-gnome (0 < 26) INFO:root:holding back phased update compiz-plugins-default (0 < 26) INFO:root:holding back phased update compizconfig-settings-manager (0 < 26) INFO:root:holding back phased update gvfs (50 < 61) INFO:root:holding back phased update gvfs-backends (50 < 61) INFO:root:holding back phased update gvfs-bin (50 < 61) INFO:root:holding back phased update gvfs-common (50 < 61) INFO:root:holding back phased update gvfs-daemons (50 < 61) INFO:root:holding back phased update gvfs-fuse (50 < 61) INFO:root:holding back phased update gvfs-libs (50 < 61) INFO:root:holding back phased update libcompizconfig0 (0 < 26) INFO:root:holding back phased update libdecoration0 (0 < 26) INFO:root:holding back phased update libjavascriptcoregtk-1.0-0 (40 < 86) INFO:root:holding back phased update libnm-glib-vpn1 (0 < 56) INFO:root:holding back phased update libnm-glib4 (0 < 56) INFO:root:holding back phased update libnm-glib4:i386 (0 < 56) INFO:root:holding back phased update libnm-util2 (0 < 56) INFO:root:holding back phased update libnm-util2:i386 (0 < 56) INFO:root:holding back phased update libnm0 (0 < 56) INFO:root:holding back phased update libwebkitgtk-1.0-0 (40 < 86) INFO:root:holding back phased update libwebkitgtk-1.0-common (40 < 86) INFO:root:holding back phased update network-manager (0 < 56) INFO:root:holding back phased update python-compizconfig (0 < 26) -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1586492 Title: update-manager does not update all available packages To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/update-manager/+bug/1586492/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs