What is Wine doing when it says, "The Wine configuration in /home/user/.wine is being updated, please wait..."?

Solution 1:

When you update your system, there may be some updates for the wine package.

Since the wine programs and directories are set in your home folder, when you first start wine after an update, it updates (copies the new wine files from the installed one to your directory) so it's completely normal.

If you look under the wine folder on your $HOME doing this:

nautilus $HOME/.wine

You'll see the "virtual" hardrive that wine uses to run the windows applications. There is a drive_c folder that acts like a C: device, you can browse it and find a reproduction of a Windows System file structure. When a new version is installed in your Ubuntu, this file structure is updated with the latest versions. There's not much more I can tell you... just think of that directory as a working version of a virtual Windows installation.