I have with success used Joomla 1.5.25 and the afterburner template.
Unfortunately I am not able to see menus with the new Joomla version 2.5.3 and the newest afterburner template from 24th of february 2012? it does not show the menus.
i believe the default positions for the menu in joomla 1.5 and 2.5 are not the same.
please go to your module manager and make sure that the menus are assigned to a module position that does exist in afterburner, otherwise the menu won't display.