When on Ubuntu setting ulimits is strange enough as upstart does ignore /etc/security/limits.conf. You need to use the "limit" stanza to change any limit. But try it with Apache and it won't help as Debian invented another way to ensure Apache ulimits can be changed. So you need to always check 
/etc/apache2/envvars
which in a fresh installation contains a line 
#APACHE_ULIMIT_MAX_FILES="ulimit -n 65535"
Uncomment it to set any max file limit you want. Restart Apache and verify the process limit in /proc/<pid>/limits which should give you something like 
$ egrep "^Limit|Max open files" /proc/3643/limits
Limit Soft Limit Hard Limit Units 
Max open files 1024 4096 files
$