WordPress MU

I just only change 2 digit numbers in the upgrade-schema.php
add_option('default_post_edit_rows', 20);
add_option('posts_per_page', 5);

Admin run wp-admin/wpmu-upgrade-site.php
"All done!"

after that, I check my user blog bottom of page the link to "Next" "Previous"
is missing...

or any idea to implement all themes using "pagenavi" plugin?
I so lazy to change theme by theme to wp_pagenavi();

ALL PAGE NAVIGATION missing...
help, please.

I found something!

If new user created, after his post > 5, it will show up the Previous / Next page navigation, but how come my old blog user page navigation will disappear? (after upgrade-schema above)

I can't figure how to change the core file /template-loader.php or link-template.php to integrate all themes support pagenavi.

I don't know if my issues are related to this topic, but.. we are actually working on a custom WPMU setup, and we have just noticed that *both* themes and admin navigation links are missing...

It would not be a huge problem on the frontend, we could still work it out in some way, but I just can't understand why is the navigation broken in the admin area (and also: if this is just our problem, or if it's already known).

Any hint?