So your trying to update Cygwin but it tells you processes are still running? What but I have all my Cygwin windows closed? Although you may have all the sessions closed you still have services running. The easiest way to check is by launching “Task Manager” in Windows. Cygwin is tightly coupled with Windows and services actually run in Windows and not Cygwin.
Open Task Manager and click on Services tab. In the screenshot below I highlighted cron. I have this running for backup jobs. Also, I have sshd service running, which you can see in the manager under the Name column: “cygsshd”. If your unsure what may be related to Cygwin look under Description column. If it was installed and configured by Cygwin and you did not provide a name than you will see “CYGWIN… ” The name usually begins with “cyg” as well. The cron I configured is called “cygcrond” but the service is still called cron which comes from Windows.
Shutdown your services by right clicking and selecting “Stop” on the service within Task Manger. That’s it you should be able to update at this point if not see if you have another service running you missed.