I have the following in my .htaccess file:
Options +FollowSymLinks
RewriteEngine on
RewriteRule ^directory/(.*)$ directory/index.php?id=$1
You should try adding a forward slash to the front:
RewriteRule ^/directory/(.*)$ directory/index.php?id=$1
I've been caught out with that before.
Alternatively use the RewriteLog and RewriteLogLevel to debug, and look at the Apache error and access logs for further info:
RewriteLogLevel 3
RewriteLog ${APACHE_LOG_DIR}/rewrite.log
That will leave a log file in your apache log directory. In my case that is /var/log/apache