I am having issues with multiverse, in my loaded worlds, i have command blocks that need to be on repeat (e.g world 1 has repeating command blocks) but this also affects world 2 aswell, and when I am in world 2, the command blocks from world 1 affect world 2 aswell, in my case, constantly setting the spawnpoint of a player to where they are. This is extremely frustrating and I was wondering if there was any way that this could be changed. Thanks

It's up to the commands ran on the command block to have per world support, MV shouldn't be altering other commands from vanilla/other plugins.