Lighttpd (pronounced "lighty") is an open-source web server more optimized for speed-critical environments than common products while remaining standards-compliant, secure and flexible. It was originally written by Jan Kneschke as a proof-of-concept of the c10k problem - how to handle 10,000 connections in parallel on one server, but has gained worldwide popularity. so to solve Joomla SEF Links problems you need to execute this steps
1) switch apache to lighttpd in ur VPS/VDS
go to enable FastCGI:
Domain home–Domain Features–set Number Of Fastcgi and enable FASTcgi.
very important: if you enable Xcache, please must set the number to 1, otherwise your RAM will be eaten by many zombie.
To check this, run “netstat -anpo|grep “php-cgi”|wc -l”, if the result is “0?, it means you should change your number of fastcgi process mumber.
2) Domain home–domain–Fcgi Configuration–enable
3) add this to etc/lighttpd/lighttpd.conf
4) Configure Joomla
on Joomla administrator panel, Global Configuration–SEO Settings–enable “Use Apache mod_rewrite” and “Search Engine Friendly URLs”, and in SH404SEF Configuration, select “with .htaccess(mod_rewrite)”.
If you enable Joomla cache, you may can not delete the cache files on “Clean Cache”. In this case, go to Kloxo File Manager, deleted all cache files.