thanks for reaching out about these issues!
Let me go through them one by one:
1) 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.
That is a vanilla thing, i am not aware of an easy way to fix this.
2) Levels are not kept on death with the Premium rank.
Do we mention this as a perk anywhere?
I am not aware of it and do not see it mentioned anywhere...
3) /nick command doesn't work.
After some testing the command seems to work, but it does not show the nickname. Is this what you are talking about?
I will look into that.
4) 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.
Should be fixed 🙂