Just confirming that this seems to be an issue for me as well. Then again, it might just be a coincidence that only my largest ship is unable to be spawned.
Also, you can still use a shop from one of its ends (or at least that was the case with the one I was using) where there\'s hardly any possibly interfering blocks and it doesn\'t seem to work there either. I don\'t think it\'s an issue of there being a lack of room to spawn.