second attempt at typing this! Bah!
I read Mamaestes post with interest because we have had similar issues. We've been running a WPMU setup for several years and upgraded it directly to WP3.0 and WP3.1.
We noticed after a while (mainly because we don't touch the 'top level' blog much) that the platform isn't behaving correctly where the main blog is concerned.
a) like mamaestes (but perhaps not the same) our plugins page for the first blog doesn't load when you hit the 'plugins' link in the LSH nav menu. Instead you get the 'edit plugin' page for whatever the first activated plugin happens to be.
b) Menus disappears completely from the LHS Nav.
For all other blogs hosted - these are present and correctly direct you to
/plugins.php and /menu.php respectively. We can still put these in by hand on the first blog- but its a bit of a pain, and worse - some plugins just don't work correctly
Happily (kind of...) one of the plugins helped shed some light I believe, in as much as it complained about blog ID 1. AFAIK in WPMU the prima blog had ID0, so I'm going to make a leap and say perhaps its still ID0 post-upgrade -= instead of the newer idea of your prime network blog being ID1 under WP3.x
Would that be likely Andrea?
If so - the only thing we can think to do Andrea is either
a) carry on limping or
b) create a brand new install and manually export and import the content (and all the plugins, people and so on *groan*) in the hope that the new copy would employ expected Blog ID's.
Or... well, once again Flabber=Gasted, so any light you might shed much appreciated.