I don't believe any of the skins including custom standard view skins are part of or included in the backup/restore process, since on Windows at least they reside in the main install directory. You'll have to manually migrate those over.
Really wish custom skins could be put somewhere in the J River folder in %APPDATA% and could be used that way, maybe in a Custom Skins directory or something (so it doesn't interfere with the stock MC skins in the Skins folder on Mac and Linux which are in the application data folder). Then they could be included in the library backup and restore process. Would also help having skins in a directory that you don't need administrator rights to open the main.xml file in a text editor to make changes when creating a new skin.
Ideally I'm thinking the folder in the %APPDATA%\J River folder could be called Custom Skins and inside that could be the Playing Now Popup, Standard View and Theater View folders used only for custom skins. Then that folder could be backed up and restored with that data included, without messing with the stock skins on Mac and Linux.
Thoughts?