Deactivating Buddypress Using MultiDB 3.0 Creates Unworkable WP-ADMIN

I suspect multidb is having a major compatible problem with Buddypress! Or I could be wrong completely! Still, I like to give this problem some voice in hope that someone smarter than I may figure out what is going on if the same thing is occurring with him/her.

So what on earth? The problem is that if I deactivate Buddypress, when network reactivate Buddypress, the backend of wp-admin is completely screw. By this I mean in option page, nothing can be saved, links in plugin page that connect to discovered categories such as active, inactive, network, drop-ins, may work incorrectly as these appear to be redirected incorrectly as in broken links.

My setting of installation should be fine since I have the latest of everything: I'm using WordPress 3.0, Buddypress 1.2.5.2, Multi-DB 3.0, latest apache, latest php, latest OS, latest of everything else!

For your information: I've always been deactivating all other plugins before I even attempting to deactivate Buddypress. This means, it's not a plugin problem either!

All files and folders within my installations have correct permissions, and these are 644 for files, and 755 for directories. .htaccess is in the right place with right information.

Notice, after the deactivation of Buddypress and things went to hell, a simple solution to quick fix is to remove Buddypress completely! Does this mean Buddypress is the main culprit?

Also, so far the only way I can ever update Buddypress since this weird issue with the deactivation of Buddypress happens (it may very well be after the upgrades of multi-db 3.0 and wordpress 3.0), is to not deactivate Buddypress at all, but to overwrite Buddypress's directories and files with newer version.

So please, advice me on this? To my knowledge, usually it's best to deactivate Buddypress, completely delete buddypress plugin in wp-content/plugins/ and then replace the removed buddypress with newer buddypress files and directories. Since deactivating Buddypress will completely screw up the whole installation and wp-admin, the only way to update is to overwrite buddypress (but only after deactivating all plugins and removed all mu-plugins). So please, anyone has an idea how to fix this problem so my updating process in the future will be more aligned with the normal procedure that has always been the case? Thanks!