supermango and George Lerner, thank you for replying. Please bear with me on this one :-)
The problem I described in the previous posts was in an internal test-environment. Now I brutally migrated two of my WordPress sites to a multisite; saotn.org and itfaq.nl. Time to break stuff to get to the bottom of this ;-)
One thing I did different now, as opposed to last time, is I installed the WordPress MU Domain Mapping plugin through the WordPress Dashboard, as where I used the "mu-plugin" method the previous time. The process wasn't much different, and after setting up my sites ( http://www.saotn.org as ID 1, and http://www.itfaq.nl as ID 3, after deleting the site once ), I couldn't log in and the Chrome Webmaster tools showed my a cookie conflict. The cookie was still set on .saotn.org
even though I wanted to log in on my child site itfaq.nl.
So I looked at the sunrise.php file and noticed some queries on the
$wpdb->prefix_domain_mapping
$wpdb->prefix_domain_mapping_logins
tables. Which were empty in my database...
Adding, editing and deleting sites didn't change anything, the domain_mapping tables stayed empty. So I added some data with the following SQL statements:
INSERT INTO wp_sys_domain_mapping(id,blog_id,domain,active) VALUES (default,1,"www.saotn.org",1)
INSERT INTO wp_sys_domain_mapping (id, blog_id, domain, active) VALUES (default,3,"www.itfaq.nl",1)
INSERT INTO wp_sys_domain_mapping_logins (id, user_id, blog_id, t) VALUES (1,1,1,now())
INSERT INTO wp_sys_domain_mapping_logins (id, user_id, blog_id, t) VALUES (2,1,3,now())
Resulting in a successful log in to my child site itfaq.nl, sweeeet! :-)
Don't know why the tables stayed empty though, PHP didn't log any errors (error_reporting on). Maybe someone can reproduce this, preferably on Windows Server IIS, otherwise I'll mark this topic as resolved later.