Katrock - By "manual install" I assume you mean copy & pasting everything? Did you have a chance to read through lifeinthegrid's extensive documentation? http://support.lifeinthegrid.com/knowledgebase.php?category=4 Of course immediately after posting I came across it (either lack of sleep or murphy's law played a role in this)
Oh and Mr. LifeintheGrid, major props to you and your work on Duplicator. Not to mention your plethora of hearty content via your site. My arsenal of tools just got that much more hardy.
I rarely work with GoDaddy, that is if I can avoid it. If I had an account I would throw you a dummy site to test on. After reading through your documentation and digging around in your plugin, it would not surprise me if it was a permissions error as you stated.