WP 3.21 with BuddyPress 1.9 on sub directory site gives page not found errors

Set Up
Server :
PHP 5.2.15 with MySQL version: 5.0.92-community-log

Word Press Installation:
WP3.2.1 Multi site (subdirectory) BuddyPress plugin 1.9 (network enabled) + other plugins
Primary site WP3.21: running as WP site
Subdirectory site: Buddypress running

I auto upgraded WP 3.1 to WP 3.2 and BP 1.8 to 1.9 and from then on BuudyPress gave Page Not Found errors for main navavigation links (links to static pages OK)
Re-auto intalled WP3.2, manually reinstalled BP1.9 No Change. Upgraded WP to 3.2.1 No Change. I have tried disabling plugins and using the BP default theme – no change.

I tried enabling the Buddypress theme on my primary site and all the BP navigation links work correctly.

So my question is, why don’t the navigation links work on the secondary site?

I have tried to get help from the Buddypress forums but as yet, nobody offers an answer.

My Ht Access file is as follows:

# BEGIN WordPress
RewriteEngine On
RewriteBase /now/
RewriteRule ^index\.php$ – [L]

# uploaded files
RewriteRule ^([_0-9a-zA-Z-]+/)?files/(.+) wp-includes/ms-files.php?file=$2 [L]

# add a trailing slash to /wp-admin
RewriteRule ^([_0-9a-zA-Z-]+/)?wp-admin$ $1wp-admin/ [R=301,L]

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ – [L]
RewriteRule ^[_0-9a-zA-Z-]+/(wp-(content|admin|includes).*) $1 [L]
RewriteRule ^[_0-9a-zA-Z-]+/(.*\.php)$ $1 [L]
RewriteRule . index.php [L]

# END WordPress

Any help or suggestions as to what I should be looking at, are very welcome.