I agree that I "shouldn't" need to do anything but run the script. However, it didn't work.
I'm running Moodle 1.9.9 and the host uses php 5.0. Not sure what our host servers are but I had called them about any potential authorization issues as I had previously mentioned I had concerns about this and they assured me that there should not be any. In fact, I can go into MySQL and create the indexes manually with no problem. And, yes, I'm using certificate.. not fat certificate.
I did get this to work but modifying the install.xml file to ignore that table (after I had successfully loaded the table) and I achieved a successful load. I then went in and manually created the indexes and also created the ID link between the 3 tables. I ran a test and it seems to have worked and it created a table entry into all 3 tables.