Sometimes you simply have to try again. Usually two or three times should suffice though.
You can also create special vorpX shortcuts, that hook a game in another and more reliable way. Right-click the vorpX tray icon and select “Create Desktop Shortcut”, then select the .exe you want to start. This will create a shortcut on the desktop, as the menu entry title suggests. ;)
While using these shortcuts it might make sense to pause the ‘watcher’, also via the right click menu of the tray icon.
Unfortunately these shortcuts do not work well with many Steam games, but it’s always worth a try.