A few small things mostly relating to the perks from ranks:
Switching dimensions disables flight even though the command is enabled, so in order to fly again you must disable and re-enable it after switching dimensions.
Levels are not kept on death with the Premium rank.
/nick command doesn't work.
Items bought in the spawn shop are renamed so don't always work in recipes involving machines. They also don't stack in storage, nor do they work when trying to autofill from JEI from a crafting recipe.