After hours of reading the code, I found that Tex are using system() to call run the shell command.
After remove "system" from the disable_functions= from php.ini, my lex notation now working.
FYI:
I am using Debian 6.0
These are extra packages that I have installed and steps to make tex filter worked.
apt-get install texlive-full
apt-get install imagemagick
vi /etc/php5/fpm/php.ini
Change this
#disable_functions = exec,system,passthru,shell_exec,escapeshellarg,escapeshellcmd,proc_close,proc_open,dl,popen,show_source
disable_functions = exec,passthru,shell_exec,escapeshellarg,escapeshellcmd,proc_close,proc_open,dl,popen,show_source
Hope this help.