After installing an updated .htaccess that has re-write rules and such for scripts such as Joomla or Drupal I see that scripts installed in sub-directories (e.g. /webmail, /mysqladmin) no longer work.
In most cases, this issue can be fixed by adding the following line to the .htaccess file in the sub-directory:
If there is no .htaccess file, create one and put the above line in it. Note that if the script in question requires a special .htaccess that contains rewrite rules, than this solution will not work.