I got this message on my Mac again yesterday when I synced my iPhone (via USB cable), and as @Simon mentioned, the dialogue window is non-standard. The updater progress claimed it was going to take 2 minutes, but instead took over 30 minutes, moving in irregular starts and stops (1 minute 27 seconds, progressing for a few seconds, stopping again, etc.).
I let it run on its own, and it did eventually finish, but I found the process a bit weird.