Plugin activate/deactivate mixed up

I recently updated my website to use WordPress’s new Multisite functionality. I renamed the plugins folder to a temp name when I couldn’t login after installing what I thought was faulty plugin following the advice here. (Turns out, it wasn’t because of faulty plugin but because of my HTTPS — my bad.)

Anyway, now everything seems to be ok except that on the Network admin page, all deactivated plugins are actually activated in the network sites dashboard and vice-versa. Anyway I can reset this? Not really sure how to report this bug, too.