Ok, think I fixed it, but it made the script much more complicated.
Went to a variable system of keep score and moved the "flag destroyed" and "flag saved" shouts to separate encounters.
Will test it tonight. If anybody has any other suggestions, I'm open to them.
Spoiler
Story: ctf_1_flag_defend_rr_v3
Starting Encounters: 1fd_00, HK1
############################
#
# 1 Flag Defend
# Players must protect their flag from hordes of enemies
#
# Character Swaps
# Round 1, 2, 3 - thug_with_gun, thug_with_grenade, thug_with_bat
# Round 3, 4, 6 - thug_with_gun, thug_with_grenade, thug_with_bat, mafioso
# Round 7, 8, 9 - mafioso, pin_stripe
#
#
# Version 2 - removed start at distance actions
# Version 3 - switch to variable scoring system
##############################
#############
# Round 1
# Score 0 - 0
#############
Encounter: 1fd_00
Type: Custom
Actions: villains fight heroes, allies fight villains, villains attack object, villains start immediately, minions start immeditance, villains start immediately, minions start immediately
Minions: thug_with_gun, thug_with_grenade, thug_with_bat
Objects: nw_military_hut_flag
Next: If Objects Lost: destroy, score1fd_01, HK1
Next: If Objects Saved: save, score1fd_10, HK1
Alert Cutscene:
narrator says, "CTF Game Mode 1 Flag Defend."
narrator says, "The score is 0-0"
narrator says, "first to 5 wins"
narrator says telepathically, "protect your flag!"
Set Lighting to day
yellow arrow on object
##############################################
#############
# Round 2
# Score 1 - 0
#############
Encounter: 1fd_10
Type: Custom
Actions: villains fight heroes, allies fight villains, villains attack object, villains start immediately, minions start immeditance, villains start immediately, minions start immediately
Minions: thug_with_gun, thug_with_grenade, thug_with_bat
Villains: thug_with_gun, thug_with_bat
Objects: nw_military_hut_flag
Next: If Objects Lost: destroy, score1fd_11, HK1
Next: If Objects Saved: save, score1fd_20, HK1
Alert Cutscene:
narrator says, "The score is 1-0"
narrator says, "first to 5 wins"
yellow arrow on object
##############################################
#############
# Round 2
# Score 0 - 1
#############
Encounter: 1fd_01
Type: Custom
Actions: villains fight heroes, allies fight villains, villains attack object, villains start immediately, minions start immeditance, villains start immediately, minions start immediately
Minions: thug_with_gun, thug_with_grenade, thug_with_bat
Villains: thug_with_gun, thug_with_bat
Objects: nw_military_hut_flag
Next: If Objects Lost: destroy, score1fd_02, HK1
Next: If Objects Saved: save, score1fd_11, HK1
Alert Cutscene:
narrator says, "The score is 0-1"
narrator says, "first to 5 wins"
yellow arrow on object
##############################################
#############
# Round 3
# Score 2 - 0
#############
Encounter: 1fd_20
Type: Custom
Actions: villains fight heroes, allies fight villains, villains attack object, villains start immediately, minions start immeditance, villains start immediately, minions start immediately
Minions: thug_with_gun, thug_with_grenade
Villains: thug_with_gun, thug_with_bat, thug_with_gun, thug_with_grenade
Objects: nw_military_hut_flag
Next: If Objects Lost: destroy, score1fd_21, HK1
Next: If Objects Saved: save, score1fd_30, HK1
Alert Cutscene:
narrator says, "The score is 2-0"
narrator says, "first to 5 wins"
yellow arrow on object
##############################################
#############
# Round 3
# Score 1 - 1
#############
Encounter: 1fd_11
Type: Custom
Actions: villains fight heroes, allies fight villains, villains attack object, villains start immediately, minions start immeditance, villains start immediately, minions start immediately
Minions: thug_with_gun, thug_with_grenade
Villains: thug_with_gun, thug_with_bat, thug_with_gun, thug_with_grenade
Objects: nw_military_hut_flag
Next: If Objects Lost: destroy, score1fd_12, HK1
Next: If Objects Saved: save, score1fd_21, HK1
Alert Cutscene:
narrator says, "The score is 1-1"
narrator says, "first to 5 wins"
yellow arrow on object
##############################################
#############
# Round 3
# Score 0 - 2
#############
Encounter: 1fd_02
Type: Custom
Actions: villains fight heroes, allies fight villains, villains attack object, villains start immediately, minions start immeditance, villains start immediately, minions start immediately
Minions: thug_with_gun, thug_with_grenade
Villains: thug_with_gun, thug_with_bat, thug_with_gun, thug_with_grenade
Objects: nw_military_hut_flag
Next: If Objects Lost: destroy, score1fd_03, HK1
Next: If Objects Saved: save, score1fd_12, HK1
Alert Cutscene:
narrator says, "The score is 0-2"
narrator says, "first to 5 wins"
yellow arrow on object
##############################################
###########################
#
# RESET Encounter
# restarts mission from beginning after player returns to fortress
#
##############################
Encounter: reset_l
Type: cutscene
Next: reset
start Cutscene:
narrator says telepathically, "you lost the game!"
narrator says telepathically, "return to the fortress to reset and play again or choose a new game map."
################################
Encounter: reset_w
Type: cutscene
Next: reset
start Cutscene:
narrator says telepathically, "you won the game!"
narrator says telepathically, "return to the fortress to reset and play again or choose a new game map."
################################
Encounter: reset
Type: cutscene
Map: ctf_fortress
Next: 1fd_00, HK1
start Cutscene:
narrator says telepathically, "Game Mode 1 Flag Defend Reset Successfully. You may return at any time."
################################
###########################
#
# Hunter Killer Encounters
# Just here to make life more difficult
#
############################
Encounter: HK1
Type: custom
Actions: villains fight heroes, allies fight villains, villains hunt heroes, villains start immediately, minions start immediatnce, villains start immediately, minions start immediately
Villains: thug_with_gun, thug_with_grenade, thug_with_bat, thug_with_bat
Next: none
#################################
Encounter: HK2
Type: custom
Actions: villains fight heroes, allies fight villains, villains hunt heroes, villains start immediately, minions start immediatnce, villains start immediately, minions start immediately
Villains: thug_with_gun, thug_with_grenade, thug_with_bat, mafioso
Next: none
###################################
##########################
#
# destroy and save
# shouts out whether your flag was saved or destroyed
#
#########################
Encounter: destroy
Type: cutscene
Next: none
Alert Cutscene:
narrator says telepathically, "your flag was destroyed!"
############
Encounter: save
Type: cutscene
Next: none
Alert Cutscene:
narrator says telepathically, "you saved your flag!"
###################################
##############################
#
# Scoreboard
# Placeholders keep track of score
#
#############################
Encounter: score1fd_01
Type: none
Next: 1fd_01
###
Encounter: score1fd_10
Type: none
Next: 1fd_10
#######
Encounter: score1fd_20
Type: none
Next: 1fd_20
#######
Encounter: score1fd_11
Type: none
Next: 1fd_11
#######
Encounter: score1fd_02
Type: none
Next: 1fd_02
########
Encounter: score1fd_30
Type: none
Next: 1fd_30
########
Encounter: score1fd_21
Type: none
Next: 1fd_21
########
Encounter: score1fd_12
Type: none
Next: 1fd_12
########
Encounter: score1fd_03
Type: none
Next: 1fd_03
########