I'm going to go out on a limb and say it:
The WordPress MU 2.8.4a installer is broken.
This cannot be an isolated problem related to my installation, and I can't be the only person finding this. I started with an empty DB, empty .htaccess file, all perms set correctly, and this problem recurs every time I attempt to install.
When I do a stock install of WPMU 2.8.4a, the installer creates a new user, a new blog, and a new site, in addition to other ancillary information. However, these entries make no sense, and result in the dreaded The blog you have requested is not installed properly. Please contact the system administrator..
The new user record for "admin" has an ID of 2 (not 1).
The new blog created has a blog_id of 2, and points to a site_id of 1. However, the only record in the wp_site table has an ID of 2, so the very first blog created by the installer belongs to a site that does not exist.
Also, the site meta table is populated with data for a single site, with Site ID of 1, which again, does not exist.
Blog ID of 2, Site ID of 1
select * from wp_blogs;
+---------+---------+-------------------+------+--------+
| blog_id | site_id | domain | path | ...etc |
+---------+---------+-------------------+------+--------+
| 2 | 1 | thedomainname.com | / | ...etc |
+---------+---------+-------------------+------+--------+
Site ID of 2
select * from wp_site;
+----+-------------------+------+
| id | domain | path |
+----+-------------------+------+
| 2 | thedomainname.com | / |
+----+-------------------+------+
select * from wp_usermeta;
+----------+---------+-------------------+---------------------------------+
| umeta_id | user_id | meta_key | meta_value |
+----------+---------+-------------------+---------------------------------+
| 2 | 2 | nickname | admin |
| 12 | 2 | rich_editing | true |
| 22 | 2 | comment_shortcuts | false |
| 32 | 2 | admin_color | fresh |
| 52 | 2 | primary_blog | 2 |
| 62 | 2 | source_domain | thedomainname.com |
| 72 | 2 | wp_2_capabilities | a:1:{s:13:"administrator";b:1;} |
| 82 | 2 | wp_2_user_level | 10 |
+----------+---------+-------------------+---------------------------------+
Site Meta table pointing to Site ID of 1, which doesn't exist
+---------+---------+-------------------+--------+
| meta_id | site_id | meta_key | etc... |
+---------+---------+-------------------+--------+
| 2 | 1 | site_name | ... |
| 12 | 1 | admin_email | ... |
etc..., etc...
I think your project is great, guys, but this installer bug is pretty serious. Are there any patches available for this that I may have missed?