Not sure if anyone noticed this one or not. I think this issue will be specific to 3.0 ONLY WordPress Mu due to the new Capabilities made available to Administrator Role with this release:
Here is the issue:
Theme Options and Custom Homepage are not accessible to regular Blog Administrator (not the Super Admin). I have tested this on different hosting accounts and with different web servers (nginx and apache (cpanel) ).
Reason behind this is that within the functions.php file of the themes listed in subject to access those pages User Role must have an edit_themes capability.
Fix for it is simple:
1. Edit functions.php file and replace this code: 'edit_themes' with 'edit_theme_options'.
2. Save file
WPMU-Nelo has 2 places to replace the code: Lines:1011 and 3108
WPMU-Dixi has 3 places to replace the code: Lines:1243, 1496, 1679
WPMU-Triden has 3 places to replace the code: Lines: 1164, 1428, 1616
This worked for me in all instances.