None of those packages look problematic. To clarify what's going on, Trisquel 8 uses MATE as its default desktop environment, whereas Trisquel 7 and earlier used GNOME. The transition is why the upgrade process is a little messy. The 'trisquel' metapackage installs everything needed for the default desktop environment. Because 'trisquel' was not installed while you upgraded, you were missing some components of the MATE desktop environment after the upgrade.
You say that you are using gnome-panel. I'm not sure how you are running it (as a startup application perhaps?) but you won't need it anymore. mate-panel should be doing that job now. If you are indeed using gnome-panel, then it might explain why the shutdown icons don't work, as they will attempt to launch GNOME's shutdown dialog instead of MATE's. Double check that mate-panel is installed, uninstall gnome-panel, and log in/or or reboot. Hopefully you will then have mate-panel running and it will work. If you still have a panel when you log in, but the shutdown/restart icons still don't work, open a a terminal with Crtl+Alt+T, type "mate-session-save --shutdown-dialog" (without the quotes) and press enter? The expected behavior is that you will be prompted to shutdown/restart/hiberate/etc. If this happens, select "Cancel", and whether or not it happens, copy (Ctrl+Shift+C) any error messages that are printed to the terminal and paste them here. If you have no panel at all when you log in, install the package 'dconf-editor' and run it. If you don't have access to the main menu, and you don't have a launcher like Synapse installed, run it from a terminal. In dconf-editor, go to org -> mate -> desktop->session -> required-components and look at the "panel" field. If the value is blank or says anything other than mate-panel, double click the field and set it to mate-panel. Then log out/in or reboot again.
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