Categories Not working after upgrade to 1.6

[vierullo]

I recently upgraded from 1.5 to 1.6

In 1.5 I had 3 root categories.

In 1.6 I see my categories along with the Home category

 

When I try to add a product it only allows me to add the product to the HOME structure.

Any of my Links that pointed to my other root categories now return Page not Found error.

 

I have tried turning on multistore but I get the same results.