I don't know anything about Wineskin but this is a client-side issue, meaning it doesn't have anything to do with the server - it's all on your side. It saves these changes to the client by writing them to configuration files when you exit the game. This is why I never /quit out of the game if I don't have to, but instead /camp desk so that it properly goes through the signout process and writes any client configuration changes that I might have made.
Macro changes are written to EverQuest\Character_server.ini, and UI changes are written to EverQuest\UI_Character_server.ini. So something you're doing is preventing the client from successfully writing to these files when you exit the game, and 99% of the time this is due to access security issues; if you install EQ into your Program Files directory, Windows will only allow the client to write to these files if the client has administrative privileges.
Are you currently able to use other characters without experiencing the same issue? If so, then that means there's something about that specific character's configuration files that either Wineskin or the client doesn't like. If this issue occurs across all characters then it's probably an issue with Mac OS not allowing Wineskin to write to those files. If it's an issue that occurs with only one character then there's something about the automatically generated configuration files for that specific character that Wineskin is having an issue with.
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