Permissions quirks for view/deleting files

While troubleshooting a problem deleting directories in C#, I noticed an interesting incongruity that I don't understand. The kind of directories I'm trying to delete are user profiles and I get permission denied for some folders and not others. Going into the profile using the Windows GUI interface, I see all the folders. Going into the profile via a cmd prompt window and typing "dir" shows me only a subset of the folders. Though I have admin rights and full permissions, I went ahead and myself the direct owner of the profile folder and all the subfolders, and the apparent discrepancy remains.

Any idea what's going on, or what's not set right?

Thanks,
Rob Tanner