I newly upgraded a expression engine powered site from 2.1.x to 2.5.x by followed the guide on there site. It went good except for the admin menu items for the addons. For example the site uses Structure module and after the installation it still points to index.php. Every other item in the menu that isn't an add-on points to admin.php. Do any one have a solution for this problem?
It sounds like you have to remove and re-add the quick tabs (the extra buttons in the menu bar). The locations to those include a file name in the database, so they might not have changed from index.php to admin.php.
Go Members → View All → Username → Main Menu Manager. For any troublesome buttons, empty out the Title field and click Update. That'll remove the button.
Then navigate back to the add-on (aay, Add-ons → Modules → Structure) and then click the "+ Add" link in the menu bar to add it back with the updated admin.php link.