The SNAPSHOT-version seems to have fixed it, I'll keep an eye on it.
Hm, but the message is created by KeePass not KeeAgent in ProtectedDialog.cs HandleUnexpectedDesktopSwitch. It seems to me that the ProtectedDialog does not keep track of its instances. KeeAgent only triggers mainWindow.OpenDatabase(document.LockedIoc, null, false); it has no knowledge of the unlock dialog.
Repeated Secure Desktop Notification