I suggest downloading a fresh copy of Moodle and starting again. That will take out any corruption possibilities and force the site through a new upgrade. BEFORE you run the upgrade, make sure that you copy over the folders for your themes and plugins (from your original Moodle installation, not the new one that doesn't work correctly.) Check the permissions are correct.
When you run the upgrade, pay particular attention to the plugins page. Make sure that you are not missing any dependencies - if you see anything listed as missing, go back to your file manager and copy over the necessary folders and then reload the plugins page. Once this is clean with no missing stuff, go through the upgrade.
Hopefully this will clean everything up for you. If not, come back here with specific problems again.
by Emma Richardson.