Yes, I had the same problem. After waiting a little longer, I successfully updated to the newest release.
PS As you noted (and I learned), if you get the Modify, Repair, Delete box, that means it is trying to install the same version as you already have.
program updater file may have been still syncing to the server when you tried to download it. try again. If you still have trouble, please let our team know at support@comicbase.com