Clarification as requested:
From the first post, it sounds more like the upgrade had maybe not gone through properly and so I wondered if maybe something had not gone right in the process. When you upgrade your Moodle installation, before running the upgrade, you need to copy across all your plugins (additional blocks/mods/filters etc) to the new Moodle folder. Normally I will copy everything over and then on Linux run chown -R www-data:www-data to apply ownership of the whole moodle folder and all subfolders etc to the apache user and then run chmod -R 755 to apply permissions. Only then do I go the web interface and let the installer run.