When you quit Versions, there may still be some Subversion activity in progress. This can include an update or commit action that you started, as well as automatic refreshes of the change counters in the bookmarks list.
By default, Versions waits for the graceful termination and cleanup of all background activity and server connections. This usually takes just a second or so, but may take up to a couple of minutes when there is a lot going on. You can skip this wait and force background activity to be terminated immediately by clicking the “Quit Now” button.