In Magento Enterprise Edition 1.11 we have the URLs did the following
Category Lv 1 - http://me.dev.local/men-s
Category Lv 2 - http://me.dev.local/men-s/clothing
Category Lv 3 - http://me.dev.local/men-s/clothing/activewear
Product - http://me.dev.local/men-s/clothing/activewear/shirt-001
since upgrading to 1.13, the URLs no longer do this, instead it's only really the last element that is in the url (ie. men-s, activewear, shirt-001)
now i found an option in System > Configuration > Catalog > Catalog > Search Engine Optimizations called "Use Categories Path for Product URLs", setting this to Yes allowed the products to work like they did before in 1.11
with some of the categories we have, using the same example as above we have a Men's and Women's Level 1 Categories, both would have Clothing, both would have Activewear, because of the upgrade to 1.13, one fo the 2 categories is now has a -# at the end (in most cases it's -1 but we also have kids categories so some get a -2 or -3)
i am wondering if there is a setting to get Categories to have the URL Path like what i have listed above to appear like that in 1.13