Where did you get the error that you mentioned here? If it was while editing the file upload preferences and setting the server path to the upload directory, that error is likely caused by the open_basedir restriction. Also, if the new site you’re creating is copying over settings from a site with paths of your file upload preferences are currently set to ‘/’, that could be the cause of the errors you posted here. It could very well be the reason Media Temple keeps saying that your application is trying to access ‘/’.
What are the file upload paths that you have actually saved in the CP?