I am assuming you have some famillarity with hand tuning your auto-generated nav file. An auto-generated nav file should always be hand tuned. It would be better named; a half a nav file. The auto-gen rarely meshes ladders. They should always be hand tuned by the mapper to insure his map can be used by the AI.

If you don't know how to turn on your nav editor see the blog on my profile page here nav_list on the banana for a complete nav_command_list.

If you need further instruction go to this video tutorial tutorial It may be a little easier to figure out.

If a ladder starts on the first floor, and goes past the second floor to the roof, the AI will not be able to stop on the second floor. the ladder has to be divided into 2 sections. One section that starts on the first floor and stops on the second floor. And a second ladder section has to go from the second floor to the roof.

You must create these 2 sections by hand the nav_build_ladder command will just make one continuous ladder from the first floor to the roof.

Start flush with the floor on the second floor and invoke the nav_begin_area command on one hand-rail of the ladder move your cursor to the other hand-rail. Descend the ladder until the area you created is close to the ground then invoke the nav_end_area command. The new ladder should connect somewhere, be certain it is a valid area if not delete the connection and connect the ladder properly. Use the nav_dont_hide comand in the box at the bottom of the ladder to keep the bots from clustering and jamming up the ladders usability.