In my Level (104) I have two message boxes but only one message (message 1) will be displayed not only on the message box one but also in the message box 2. Shouldnt message box 2 usually display message 2?
It could be because level 104 is by default, a "special message" level (Yoshi's house). Go to the overworld editor, click on Overworld -> "Change Special Message Levels...", and then change the "Yoshi's House" option to something other than 104. I'm not sure if this is the solution but it's the first thing that comes to mind.
It means that some messages have an additional (hardcoded) property in the vanilla game, and the LM window allows you to change in which level the property will apply. For example, message 2 in level 104 (Yoshi's House) is normally hardcoded to only show up when you're riding Yoshi. Instead the Switch Palace messages have the additional property of making the "!" Blocks appear inside the message.