If you are using fcgi and mpm-worker mode with your apache. You will probably need to set some variables to make your drupal sites work. As they have some stupid defaults like 128kb upload limit (really 128 kb today?) and they override your php.ini settings as now PHP is running trough this FCGI, then you need to go to
/etc/apache2/mods-available/fcgid.conf if there is where your FCGID mod is installed and then change conf file. Just add simple line of with your number of bytes
FcgidMaxRequestLen 1073741824for other settings look them all here http://httpd.apache.org/mod_fcgid/mod/mod_fcgid.html
and some useful suggestions in comments here
http://2bits.com/articles/apache-fcgid-acceptable-performance-and-bette…
Also now php.ini settings are in /etc/php5/cgi and not the ones in php5/apache2 directory, so be sure to change data.