That is so strange. My Mianne lift gate has never had an issue not seating. It does have a lot of weight on it with the 3/4inch plywood top, the track and scenery so maybe that helps. My cable never loses tension. Even down it has some tension on it, so it can't come off the pulleys. I think my adjustment for the lower limit is just a hair past the stop so it keeps tension on the cable. So its kind of like it tugs a little on the cable after the top fully seats down. I didn't have to go through all the stuff you described. Perhaps you installation is not perfectly square and it is racked a little. I could see where that would cause it not to seat all the way. I tested the gate without the cable first, manually pushing it up and then dropping it down to verify it seated even before I installed the motor or cable.
If you go to time spot 18:26 in this video you can see it. Also this shows how to wire up an inside, outside control switch.
