The timing of this thread is perfect. I was checking one of my domains and found that about a year ago the URL structure was changed.
Most of the site was changed to reflect the new URL Structure, however the bottom navigation was hard coded into a module that the developer was too lazy to change, so he 301'ed 15 menu items back to home.
15 x 100's of pages = BAD NEWS. Yesterday we rectified the issue and I am interested to see the ramifications. The site is hovering 14 at the moment for a highly competitive keyword. I will keep you posted, but not sure how long it will take to reflect.