New registration process could not create the blog "and table"

the condition is weird in our Multisite.

The condition:
I used the multisite 3.1.2, (live) that hold around 30000 users and blogs (oh yes, there’s tons of spams -i’m in attitude to kill them all for several weeks later). And the company didn’t cluster/scaling database yet. Waiting the upgrade-migration process finished (that i do right now)

Its come from the old WPMU 2.7 before (i posted in this forum about our upgrade). Upgraded step by step from 2.7, 2.8, 2.9, 3.0, 3.1. Upgrading with native WP (all plugins shutting down).
It was working smoothly. They use nginx for this website

And then the problems occured:
1. The pagination in “users list” and “blog list” -network admin (navigation at the top right of table), its not working.
(this pagination problem, maybe have corelation with next problem)

2. The big problems then the visitor couldnot create new blog: (but the admin can do this like there’s no problem)
– they can register username, email, then next step choose subdomain name.
– the new registered get an email notification about activation key. The URL for wp-activation.php use subdomain.domain.com/~key. False redirect.
– So, I did small change on ms-function, to generate the correct address. So now its works for domain.com/~key.
– But then another stuck loading comes from that activation process. Its just stopped, without confirmation for new registered user.
– I check the wp_signups, users list, and blog list. Its recorded. But, the blog not working. So i check the database, darn.. the tables wp_id_ was not created.

I test it several times, with or without plugins.
Then, for backtest, i copied all core (WP-ADMIN, WP-INCLUDES) from live website, then use for test website in similar server container. I took some database sampling.
And i did the test (login, pagination).. its working fabolously like there’s no problem at all. 🙁

I did some debugging process all night, to get where is the bug, and then the die process stuck at wp-admin/includes/upgrade.php -recognized the show tables process stuck in “function dbDelta”.

So, here’s the question after long detail above, maybe some expert here can explain about the limitation and confused problem here? Or maybe there’s something i miss about the process?

Thanks you verymuch