WPMU-2.9.2 to WP-3.1


We just sucessfully(all except the issue mentioned here as far as we see now) updated WPMU-2.9.2 to WP-3.1 MultiSite.

We are using Multi-DB Version: 3.0.6.

There are 200+ users and all of them together have almost 2000+ sites while upgrading and all seem to work fine too.
All plugins work fine too now, had to update couple of them too before they did.

But, while logged in as 'admin', it says "Thank you for Updating! Please visit the Update Network page to update all your sites." << We do that and get following messages on different browsers we tried.
Get the same result when we try to access 'Network Admin' on top right of admin login.

Too many redirects occurred trying to open “http://{our-site}.com/wp-admin/network/”. This might occur if you open a page that is redirected to open another page which then is redirected to open the original page.
This webpage has a redirect loop
The webpage at http://{our-site}/wp-admin/network/ has resulted in too many redirects. Clearing your cookies for this site or allowing third-party cookies may fix the problem. If not, it is possibly a server configuration issue and not a problem with your computer.
Its still working and has not shown any messages yet, can see 'Waiting for http://{our-site}/wp-admin/network/upgrade.php' on the status bar. (I'll post update if I get any results)
Not tried yet as IE is still working on as I write this.

Kindly advice, could it be an upgrade issue or could the delay be because we have several sites and is it worth waiting for IE to show results?

Thanks & Regards