There is a new rule now in Joomla that was not in version 1.5. In order to be compliant with SEF and Google requirement to have one content per one url, and given that alias are used to build the urls, you cannot have the same alias under the same parent. That goes for menus, articles etc.
Therefore SP Upgrade when identify such case, automatically add the -sp-xxxxx to the alias. Even if you try to manually edit it from back end, you will see that Joomla will not allow it. There is a good chance, those duplicates comes from your trash. So what I suggest is to delete and empty trash for any not needed items, and repeat process from scratch. If you do not have many of these cases you may also consider the possibility to identify each duplicate and decide what to keep.