Upgraded to latest, now issues

I just upgraded to 2.0.9 by exported my file, doing the uninstalled, installed the new version, then did used the backup utility to import my file.

It still is set to NOT include Sections in the URLS, but now half of my URLs are not working.  They DO work, on the other hand, when you click on the menus, but the address is including the section.

I double-checked the settings, and everything looks as it should be (to not include the section).

Any ideas?

Those specific questions really need example URLs from the live site. I have no idea without looking at it.

Hi Emir: I have the same problem. I have deactivated Advanced SEF... tonight (UStimes) at low traffic times I will reactivate it and show you...