I’ve been having issues with the automatic update of plugins and the WordPress core files for some time now and I could never quite track it down until today.
I was at my wits end with the updater and was contemplating exporting the WordPress MySQL database and installing it on to a new install folder. My best guess was that the issue was related to a core file that wasn’t overwriting correctly from my FTP upload, as it has happened before but with other side effects. After I exported my SQL file I noticed it was 6.3MB, which is huge. I dug into the SQL table and noticed that wp_options was about 6MB alone. Further inspection showed a bunch of RSS files that turn out to be cache files that are supposed to be purged. There were also lots of references to old plugins that I no longer used. My initial thought was to manually delete these entries but there were 300+ of them and that would have taken way too long. It could have also lead to me deleting an entry that was needed. A quick Google search turned up this plugin. I deactivated my current plugins so I could activate the Clean Options Plugin (internal server errors after enabling plugins were another symptom I was seeing) and ended up cleaning up over 350 orphaned entries! The wp_options table is now down to 50KB.
Now my plugin and core updates all work correctly. My dashboard also is able to load more than just a couple widgets and in general the admin interface just works better.
While poking around 
