I can't seem to get SA to show paid invoices. I'm on all of the latest versions and walked a transaction through all of the steps including printing and clearing all posting journals. But still I get a not paid in both SA inquiry and Gridview. What am I missing?

Run the Set Paid Invoices utility to update Sales Analysis invoices with the paid status. This doesn't happen automatically when an invoice is paid in AR - you have to run the utility.