I upgraded from 3.0.5 to 3.1 manually. Everything was working great, I went to update the entire network and got:
Warning! Problem updating http://theneel.sportsblognet.com. Your server may not be able to connect to sites running on it. Error message: couldn't connect to host
So, I tried going to http://theneel.sportsblognet.com/wp-admin/upgrade.php and I was able to upgrade that individual blog without issue. However, I have 1000+ blogs and I really don't feel like doing them all individually.
I have tried disabling all plugins and renaming the mu-plugins directory. Still the same issue. I archived that first blog(http://theneel.sportsblognet.com) and it gave me the same error on the second blog it tried to update.
I have switched my theme to twenty-ten, still the same issues. My .htaccess is the same as it was before the upgrade and all of my sites work.
Also, I am missing the "Network Admin" link in the upper right hand corner. However, i can manually type in http://sportsblognet.com/wp-admin/network and get to the network section. Very strange.
Can someone help me out?