Broken SEF URL links after migrating away from SectionEx on J! 3.2.1

Hi StackIdeas,

We just had our site migrated from Joomla 1.5 to 3.2.1. The 1.5.x Joomla site was using a SectionEx menu item to display a Section-Category-Article-List. Our developer migrated the site content and set up the old SectionEx menu item as a standard Joomla Category Blog menu item.

All of the links in the Section-Category-Article-List work. We weren't using SEF URLs in the old site, but we want to do so in the new site. Problem is that when we turn on SEF URLs and enable URL Rewriting (and rename .htaccess), the majority of the old SectionEx links break in the new Category Blog menu item page.

Do you have any recommendations or protocol of how we can solve this problem?

Some of the URLs looks pretty normal:
http://www.oursite.com/site/staging/index.php?option=com_content&view=article&id=111&Itemid=473

Others look pretty strange, but they work when SEF URLs, etc. is turned off:
http://www.oursite.com/site/staging/index.php?option=com_content&view=article&id=608:this-is-the-alias&catid=23&Itemid=1626

Thanks in advance for any help!

KImo