In the primary world the one with the spawn and all that potions don't work.But in my other factions world potions work when someone is gm 1.Other stuff is blocked tho but there may be other bugs when using multiple worlds

Pastebin your config.yml and your world configurations please

http://pastebin.com/wwTkWtwN global config
http://pastebin.com/cdKq0BTD the bug world config
you can try using multi verse with 2 worlds and in the first one potions are disabled second one everything is good(havent checked,most is good) but potions work :/

btw i use authme and i think this bug is specific to authme

Cannot reproduce.

Offline mode server as well - Therefore no support.
And you are not using CraftBukkit - Therefore no support.