I looked in to it more, I suspect the firewall was dropping some connections/file downloads and no response was getting back to Launchbox. I whitelisted the IP that launchbox was using and that sped up the process (well still took hours but was moving along a bit quicker).
It would be good to have some control of the timeout if that is possible. It might be a server issue or some router along the path dropping packets/connection for someone else so it would be good to have this feature.