Working with a fresh install at http://elliotthedog.com. The install was done this morning, directly into multi site.
I performed the changes from Network as required after reference to my host, GoDaddy, and the install all seemed fine.
When I attempt to add another site, the process goes fine and all links point to the subfolder(s) to be expected. Sadly, back and front end fail to respond.
I did change the permalinks on the root by accident but changed them right back after I noticed that the pages no longer would display on the root. The pages worked, blogs do not. I deleted the blog and added it again to the root, checking the basic settings and folder paths, all looked normal. I removed it and added a fresh blog called test, it is still reporting to the root as there and working however it still will not come up in the browser for front or back end.
Aside fresh install, any other ideas?