My multiblock is not forming and I think it has to do with the brewing stand, which changes metadata along with nbtdata. No matter what I do, I cannot get it to form no matter what I try. All of my other machines are fine. Here is the .json. It is valid, and it formed a blueprint in the game. Oh, it is in 1.4
version of the mod.
https://pastebin.com/ck89EhnM

        "nbt": {"Items":[{"Slot":"0b","id":"minecraft:potion","Count":"1b","tag":{"Potion":"minecraft:water"},"Damage":"0s"},{"Slot":"1b","id":"minecraft:potion","Count":"1b","tag":{"Potion":"minecraft:water"},"Damage":"0s"},{"Slot":"2b","id":"minecraft:potion","Count":"1b","tag":{"Potion":"minecraft:water"},"Damage":"0s"}]},
        "elements": [
            "minecraft:brewing_stand"
        ]

Try not to check against the specific NBT - as it is described in the World-To-JSON tool in the wiki, doing the exporting into JSON also dumps the full NBT data fully serialized. and you might want to delete it partially or alltogether as in this example.
If the NBT-checking against the bottles inside the brewing stand is desired, then please try and reduce the amount of checks to just a part of what it is now... maybe try removing the damage number, the count, ... all that would help narrow down the amount of checks it does until we get to a point to pinpoint either which NBT-data check is failing under certain conditions.