When I am using Wine or changing its preferences, I often get a pop-up that says, "The Wine configuration in /home/user/.wine is being updated, please wait..." It stays there for a minute or two, and then disappears and whatever I wanted to do happens. Internet searches for this dialog box have only pulled up bug reports, and never an explanation of what is going on.
What "configuration" is Wine updating, and why does it have to do it so often?
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:
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.