Hi:

I first installed the latest free version on my localhost installation :
Windows XP
XAMMP (PHP 5)
Joomla 1.5.9

Worked like a charm

I then purchased the paid version for my site in development
PHP5/joomla 1.5.9
my installation is currently behind a protected directory
All menu links now report a 404 error regardless of whether they are a component or article

Any help would be greatly appreciated

Here is my htaccess file:
----------------------------------
AuthType Basic
AuthName "Access for /installation"
AuthUserFile /XXXX/htpasswd
require user XXX
require user XXX
AddType x-mapp-php5 .php
SetEnv TZ America/Los_Angeles
RewriteBase /installation


########## Begin - Joomla! core SEF Section
#
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} !^/index.php
RewriteCond %{REQUEST_URI} (/|\.php|\.html|\.htm|\.feed|\.pdf|\.raw|/[^.]*)$ [NC]
RewriteRule (.*) index.php
RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization},L]
#
########## End - Joomla! core SEF Section

--------------------------------------------------------------------------------------------------------

Check your configuration that the .htaccess file is really accepted and not overridden by some directives on other directory levels.