You’ve got a nice custom theme. What you need to do is copy/merge the contents of the standard BuddyPress theme functions.php into that of the theme you are using.
If this has already been done, check your htaccess/mod_rewrite is enabled.
everything from this file (BPmember/functions.php) into my custom functions.php file ?
I will try now
This is my htaccess
RewriteEngine On
RewriteBase /
#uploaded files
RewriteRule ^(.*/)?files/$ index.php [L]
RewriteCond %{REQUEST_URI} !.*wp-content/plugins.*
RewriteRule ^(.*/)?files/(.*) wp-content/blogs.php?file=$2 [L]
# add a trailing slash to /wp-admin
RewriteCond %{REQUEST_URI} ^.*/wp-admin$
RewriteRule ^(.+)$ $1/ [R=301,L]
RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule . – [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(wp-.*) $2 [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(.*\.php)$ $2 [L]
RewriteRule . index.php [L]
<IfModule mod_security.c>
<Files async-upload.php>
SecFilterEngine Off
SecFilterScanPOST Off
</Files>
</IfModule>
I guess mod_rewrite is enabled because it works when using permalinks in WPMU, but I turned it off because when I use it my pages wont display, but thats another problem I have.
I tried copy the content from the bpmember/bphome functions.php file into my custom functions.php file, but it didnt seem to work
I tried this today, but the links are still not valid 
you can see for yourself here http://www.librarium-online.com
Try the random member/group/blog. Its the same issue with them
1. Which version of WPMU are you running?
2.8.4
2. Did you install WPMU as a directory or subdomain install?
sub-directory
3. If a directory install, is it in root or in a subdirectory?
root
4. Did you upgraded from a previous version of WPMU? If so, from which version?
No
5. Was WPMU functioning properly before installing/upgrading BuddyPress?
Yes
6. Which version of BuddyPress (BP) are you running?
1.0.3
7. Did you upgraded from a previous version of BP? If so, from which version?
No
8. Do you have any plugins other than BuddyPress installed and activated?
Yes, domain-mapping and Disqus, FlickrRss, Akismet
9. Are you using the standard BuddyPress themes or customized themes?
Im using custom WPMU compatible theme for mainblog
10. Have you modified the core files in any way?
No
11. Do you have any custom functions in bp-custom.php?
No
12. If running bbPress, which version?
No
13. Please provide a list of any errors in your server’s log files.
none
@aero7
The first steps are to distill your install down to the lowest common denominator. That means disabling all plugins except BuddyPress and switching to the default theme framework that comes with BP. If the problem goes away, then it has something to do with your theme and/or plugins.
If that is the case, they the next step is to reactivating each plugin one at a time until the issue returns. If it does not return, then switch to your custom theme. If it returns, then there is an issue with your custom theme.
