I was checking out the Site Collection List from Central Administration for My Site and it lists everybody who has a My Site for the web application. I go to another web application and it doesn't list anything, just the root site. There are sites below the root, I created them. Any ideas on this? Thanks!

Can you browse your sites from the browser? Seems to me you may have created those as sites NOT site collections. To verify that you can browse to the root site from UI on the browser (say http:\\yoursite) and then go to View all site content (from Site Actions)? Do you see your sites listed there? Hope this helps!BlueSky2010