Do you mean?
- File > Library > Organize Library > Consolidate Files
- File > Library > Organize Library > Rearrange Files
- Edit > Preferences > Advanced > Keep iTunes Media folder organized
The first will copy any content located outside of the media folder into it. iTunes doesn't check to see if the library is currently consolidated, so that option is always available if you reopen the dialog, even if you only used it seconds ago.
Option two will put music items in a subfolder of the media folder called \Music. This option will be greyed out if it has previously been selected, and it is also the default option for a new library.
The third box should retain your setting, staying checked or unchecked if you revisit that dialog later. If your choice isn't being remembered I can suggest some files that you can delete to reset your preferences.
The other preference that is relevant here is:
Edit > Preferences > Advanced > Copy files to iTunes Media folder when adding to library
If this is checked then there is no need to repeatedly consolidate the library, as all new additions will be consolidated.
tt2