Reference: http://mu.wordpress.org/forums/topic.php?id=4519
Running wpmu-1.2.1, folder-based blogs (not subdomains).
Created a secondary domain on the wp_site table. Blogs on the primary site work OK. Admin on the secondary site works ok, can create both posts and pages. When accessing a blog on the secondary site, posts show but pages don't, unless an equally-named page exists on the primary domain.
Say I have:
domain1.com/page1
domain2.com/page1
domain2.com/page2
then domain2.com/page1 works but domain2.com/page2 doesn't (404-signup page).
If I create a domain1.com/page2 page, then domain2.com/page2 starts working. If I delete domain1.com/page1, then domain2.com/page1 stops working.