I've just been downloading the new release each time and copying over my save, not bothering with the patch files. I haven't run into any of these glitches aside from the maid scene getting stuck from the previous version.
Though I noticed that after you have the tour of the slave traders hideout and regain player control, you can return to the captain's quarters. He's sitting at his desk again, and the event plays out where he uses the device on you and leads you out of the building. Once outside however, the captain is gone and you get control back like nothing happened.