I'm probably wrong, as I am rather new to this. But did you try removing the startups sp and fire and just adding all of that script after (ai_place boss_2)?
what I mean:

(script startup poop
(sleep_until (= (ai_living_count wave_1) 0) 15)
(ai_place wave_2)
(sleep_until (= (ai_living_count wave_2) 0) 15)
(ai_place wave_3)
(sleep_until (= (ai_living_count wave_3) 0) 15)
(ai_place wave_4)
(sleep_until (= (ai_living_count wave_4) 0) 15)
(ai_place wave_5)
(sleep_until (= (ai_living_count wave_5) 0) 15)
(ai_place boss_1)
(sleep_until (= (ai_living_count boss_1) 0) 15)
(ai_place wave_6)
(sleep_until (= (ai_living_count wave_6) 0) 15)
(ai_place wave_7)
(sleep_until (= (ai_living_count wave_7) 0) 15)
(ai_place wave_8)
(sleep_until (= (ai_living_count wave_8) 0) 15)
(ai_place boss_2)
(sleep_until (= (ai_living_count boss_2) 0) 15)
(activate_team_nav_point_flag default "player" nav_1 0.6)
(game_save_no_timeout)
(ai_place pod)
(ai_place wave_9)
(ai_place gunner)
(vehicle_load_magic gun "" (ai_actors gunner/gun))
(sleep_until (volume_test_objects trigger_2 (players))15)
(deactivate_team_nav_point_flag "player" nav_1)
(sleep_until (= (ai_living_count wave_9) 0) 15)
(fade_out 0 0 0 100)
)

edit: Now that I think about it, the fact that boss_2 is not spawned at the start of the level might be part of the reason you are having problems, as your script says to to spawn the nav when boss_2 is not alive. Again, I'm probably wrong, but it's worth a try.
Edited by SAS on May 20, 2013 at 05:09 PM
Edited by SAS on May 20, 2013 at 05:15 PM

i think your problem is you used (script startup sp
startup commands are issued when the map starts you want it to activate when you tell it to.

(script dormant sp

^is how you want to start
the script will wait until called upon by

(wake script dormant sp)

im just learning scripting, but i think it would go something similar to this:

(script dormant sp
(activate_team_nav_point_flag default "player" nav_1 0.6)
(game_save_no_timeout)
(sleep_until true 1 (= (ai_living_count boss_2) 0) 15)
(if (ai_living_count boss_2) 0) 15) (wake script dormant sp)

I would use that if it was an optional waypoint. but for a linear series of events, it is easier to just continue the script as I previously mentioned. That said, I actually have never ventured into dormant scripts. I will keep this in mind whenever I do.

for future reference heres the scripting bible kornman00 wrote, it has almost all the scripting functions and variables explained.

http://www.modacity.net/docs/bslbible/