This could have been caused if you installed WP/MU via simplescripts, fantastico, etc. Delete previous installation including htaccess file generated and wp-config (if MU) and drop database tables.
Do manual upload of WP or MU via FTP or cpanel and install.
Go to dashboard > Settings > Permalinks and run it.
Do FTP/cpanel upload of BuddyPress plugin.
Activate BP plugin and go to BP settings page to enable components.