I recently ran into a problem with my Wordpress installations. I could not auto update my plugins. After some research, I found that it was a problem with the hosting server having php4 and php5 enabled at the same time. This is common practice for shared hosting plans. I found that adding the following lines to the .htaccess file will fix the problem.
Before doing this, I would recommend you backup your Wordpress installation (incl. database, files and folders).