So you changed it back to 50 civs? In a to 40 civs fixed scenario there was now 40 civs, that will meen if you have 40 civs 0-39 then you cant start new civs with the numbers 45 to 50 i think... these civs should start with 40 to 45 then... mabe theres the problem, no empty civs from 40 to 45 allowed i bet... so to fix one of these scenairos you have to add some civs from 40 to 45 to fill up the empty space... then you can start the other civs from 45 to 50...
Also there will be no civ 50 only 0-49 you can try to set babarians to 49 and the rest one lower, maybe that fix it. The 50 civ dll is only 0-49, so Babarians on 50 will not work.
Also add the empty teans to a scenario if that dont helps... they was removed...
Like:
BeginTeam
TeamID=37
ContactWithTeam=37
RevealMap=0
EndTeam
BeginTeam
TeamID=38
ContactWithTeam=38
RevealMap=0
EndTeam
BeginTeam
TeamID=39
ContactWithTeam=39
RevealMap=0
EndTeam
If you have now team 44 to 49 then theses teams 40 to 44 missing in all scenarios now that was set back from 50 civs to 40 civs. So you have no civs between 39 and 44 or you have barbarians on civ 50 but last civ/team should be 49. Try add the missing civs to a scenario or change barbarians from 50 to 49 and lower the others one team down. But maybe no empty civs under the NPC civs allowed.
Insectoids? Aliens?

Cool...
Ok i looked deeper... if i saved a new scenario with latest SVN it adds these to a scenario file:
BeginPlayer
Team=45
LeaderType=LEADER_BARBARIAN
LeaderName=TXT_KEY_LEADER_BARBARIAN
CivDesc=TXT_KEY_CIV_INSECTOID_DESC
CivShortDesc=TXT_KEY_CIV_INSECTOID_SHORT_DESC
CivAdjective=TXT_KEY_CIV_INSECTOID_ADJECTIVE
FlagDecal=Art/Interface/TeamColor/FlagDECAL_Skullcrossbones.dds
WhiteFlag=0
CivType=CIVILIZATION_INSECTOID
Color=PLAYERCOLOR_BLACK
ArtStyle=ARTSTYLE_BARBARIAN
PlayableCiv=0
MinorNationStatus=0
StartingGold=0
StateReligion=
StartingEra=ERA_PREHISTORIC
RandomStartLocation=false
CivicOption=CIVICOPTION_GOVERNMENT, Civic=CIVIC_ANARCHISM
CivicOption=CIVICOPTION_RULE, Civic=CIVIC_OBEDIENCE
CivicOption=CIVICOPTION_POWER, Civic=CIVIC_STRONGMAN
CivicOption=CIVICOPTION_SOCIETY, Civic=CIVIC_PRIMITIVE
CivicOption=CIVICOPTION_ECONOMY, Civic=CIVIC_COMMUNALISM
CivicOption=CIVICOPTION_MILITARY, Civic=CIVIC_MILITIA
CivicOption=CIVICOPTION_RELIGION, Civic=CIVIC_IRRELIGION
CivicOption=CIVICOPTION_WELFARE, Civic=CIVIC_SURVIVAL
CivicOption=CIVICOPTION_GARBAGE, Civic=CIVIC_NOTRASH
CivicOption=CIVICOPTION_IMMIGRATION, Civic=CIVIC_NOBORDERS
CivicOption=CIVICOPTION_EDUCATION, Civic=CIVIC_IGNORANCE
CivicOption=CIVICOPTION_LANGUAGE, Civic=CIVIC_NO_SPEAK
CivicOption=CIVICOPTION_AGICULTURE, Civic=CIVIC_NOFARM
CivicOption=CIVICOPTION_CURRENCY, Civic=CIVIC_NO_CURRENCY
CivicOption=CIVICOPTION_LABOR, Civic=CIVIC_UNORGANIZED
Handicap=HANDICAP_NOBLE
EndPlayer
BeginPlayer
Team=46
LeaderType=LEADER_NEANDERTHAL
LeaderName=TXT_KEY_CIV_NPC_NEANDERTHAL_DESC
CivDesc=TXT_KEY_CIV_NPC_NEANDERTHAL_DESC
CivShortDesc=TXT_KEY_CIV_NPC_NEANDERTHAL_SHORT_DESC
CivAdjective=TXT_KEY_CIV_NPC_NEANDERTHAL_ADJECTIVE
FlagDecal=Art/Interface/TeamColor/FlagDecal_Neanderthal.dds
WhiteFlag=1
CivType=CIVILIZATION_NPC_NEANDERTHAL
Color=PLAYERCOLOR_NEANDERTHAL
ArtStyle=ARTSTYLE_BARBARIAN
PlayableCiv=0
MinorNationStatus=0
StartingGold=0
StateReligion=
StartingEra=ERA_FUTURE
RandomStartLocation=false
CivicOption=CIVICOPTION_GOVERNMENT, Civic=CIVIC_ANARCHISM
CivicOption=CIVICOPTION_RULE, Civic=CIVIC_OBEDIENCE
CivicOption=CIVICOPTION_POWER, Civic=CIVIC_STRONGMAN
CivicOption=CIVICOPTION_SOCIETY, Civic=CIVIC_PRIMITIVE
CivicOption=CIVICOPTION_ECONOMY, Civic=CIVIC_COMMUNALISM
CivicOption=CIVICOPTION_MILITARY, Civic=CIVIC_MILITIA
CivicOption=CIVICOPTION_RELIGION, Civic=CIVIC_IRRELIGION
CivicOption=CIVICOPTION_WELFARE, Civic=CIVIC_SURVIVAL
CivicOption=CIVICOPTION_GARBAGE, Civic=CIVIC_NOTRASH
CivicOption=CIVICOPTION_IMMIGRATION, Civic=CIVIC_NOBORDERS
CivicOption=CIVICOPTION_EDUCATION, Civic=CIVIC_IGNORANCE
CivicOption=CIVICOPTION_LANGUAGE, Civic=CIVIC_NO_SPEAK
CivicOption=CIVICOPTION_AGICULTURE, Civic=CIVIC_NOFARM
CivicOption=CIVICOPTION_CURRENCY, Civic=CIVIC_NO_CURRENCY
CivicOption=CIVICOPTION_LABOR, Civic=CIVIC_UNORGANIZED
Handicap=HANDICAP_NOBLE
EndPlayer
BeginPlayer
Team=47
LeaderType=LEADER_GREEN_MAN
LeaderName=TXT_KEY_LEADER_GREEN_MAN
CivDesc=TXT_KEY_CIV_ANIMAL_BEAST_DESC
CivShortDesc=TXT_KEY_CIV_ANIMAL_BEAST_DESC_SHORT
CivAdjective=TXT_KEY_CIV_ANIMAL_BEAST_ADJECTIVE
FlagDecal=Art/Interface/TeamColor/FlagDecal_Beast.dds
WhiteFlag=1
CivType=CIVILIZATION_ANIMAL_BEAST
Color=PLAYERCOLOR_ANIMAL
ArtStyle=ARTSTYLE_BARBARIAN
PlayableCiv=0
MinorNationStatus=0
StartingGold=0
StateReligion=
StartingEra=ERA_PREHISTORIC
RandomStartLocation=false
CivicOption=CIVICOPTION_GOVERNMENT, Civic=CIVIC_ANARCHISM
CivicOption=CIVICOPTION_RULE, Civic=CIVIC_OBEDIENCE
CivicOption=CIVICOPTION_POWER, Civic=CIVIC_STRONGMAN
CivicOption=CIVICOPTION_SOCIETY, Civic=CIVIC_PRIMITIVE
CivicOption=CIVICOPTION_ECONOMY, Civic=CIVIC_COMMUNALISM
CivicOption=CIVICOPTION_MILITARY, Civic=CIVIC_MILITIA
CivicOption=CIVICOPTION_RELIGION, Civic=CIVIC_IRRELIGION
CivicOption=CIVICOPTION_WELFARE, Civic=CIVIC_SURVIVAL
CivicOption=CIVICOPTION_GARBAGE, Civic=CIVIC_NOTRASH
CivicOption=CIVICOPTION_IMMIGRATION, Civic=CIVIC_NOBORDERS
CivicOption=CIVICOPTION_EDUCATION, Civic=CIVIC_IGNORANCE
CivicOption=CIVICOPTION_LANGUAGE, Civic=CIVIC_NO_SPEAK
CivicOption=CIVICOPTION_AGICULTURE, Civic=CIVIC_NOFARM
CivicOption=CIVICOPTION_CURRENCY, Civic=CIVIC_NO_CURRENCY
CivicOption=CIVICOPTION_LABOR, Civic=CIVIC_UNORGANIZED
Handicap=HANDICAP_NOBLE
EndPlayer
BeginPlayer
Team=48
LeaderType=LEADER_GREEN_MAN
LeaderName=TXT_KEY_LEADER_GREEN_MAN
CivDesc=TXT_KEY_CIV_ANIMAL_PREDATOR_DESC
CivShortDesc=TXT_KEY_CIV_ANIMAL_PREDATOR_DESC_SHORT
CivAdjective=TXT_KEY_CIV_ANIMAL_PREDATOR_ADJECTIVE
FlagDecal=Art/Interface/TeamColor/FlagDecal_Predator.dds
WhiteFlag=1
CivType=CIVILIZATION_ANIMAL_PREDATOR
Color=PLAYERCOLOR_NEANDERTHAL_EMPIRE
ArtStyle=ARTSTYLE_BARBARIAN
PlayableCiv=0
MinorNationStatus=0
StartingGold=0
StateReligion=
StartingEra=ERA_PREHISTORIC
RandomStartLocation=false
CivicOption=CIVICOPTION_GOVERNMENT, Civic=CIVIC_ANARCHISM
CivicOption=CIVICOPTION_RULE, Civic=CIVIC_OBEDIENCE
CivicOption=CIVICOPTION_POWER, Civic=CIVIC_STRONGMAN
CivicOption=CIVICOPTION_SOCIETY, Civic=CIVIC_PRIMITIVE
CivicOption=CIVICOPTION_ECONOMY, Civic=CIVIC_COMMUNALISM
CivicOption=CIVICOPTION_MILITARY, Civic=CIVIC_MILITIA
CivicOption=CIVICOPTION_RELIGION, Civic=CIVIC_IRRELIGION
CivicOption=CIVICOPTION_WELFARE, Civic=CIVIC_SURVIVAL
CivicOption=CIVICOPTION_GARBAGE, Civic=CIVIC_NOTRASH
CivicOption=CIVICOPTION_IMMIGRATION, Civic=CIVIC_NOBORDERS
CivicOption=CIVICOPTION_EDUCATION, Civic=CIVIC_IGNORANCE
CivicOption=CIVICOPTION_LANGUAGE, Civic=CIVIC_NO_SPEAK
CivicOption=CIVICOPTION_AGICULTURE, Civic=CIVIC_NOFARM
CivicOption=CIVICOPTION_CURRENCY, Civic=CIVIC_NO_CURRENCY
CivicOption=CIVICOPTION_LABOR, Civic=CIVIC_UNORGANIZED
Handicap=HANDICAP_NOBLE
EndPlayer
BeginPlayer
Team=49
LeaderType=LEADER_GREEN_MAN
LeaderName=TXT_KEY_LEADER_GREEN_MAN
CivDesc=TXT_KEY_CIV_ANIMAL_PREY_DESC
CivShortDesc=TXT_KEY_CIV_ANIMAL_PREY_DESC_SHORT
CivAdjective=TXT_KEY_CIV_ANIMAL_PREY_ADJECTIVE
FlagDecal=Art/Interface/TeamColor/FlagDecal_Creature.dds
WhiteFlag=1
CivType=CIVILIZATION_ANIMAL_PREY
Color=PLAYERCOLOR_MAORI
ArtStyle=ARTSTYLE_BARBARIAN
PlayableCiv=0
MinorNationStatus=0
StartingGold=0
StateReligion=
StartingEra=ERA_PREHISTORIC
RandomStartLocation=false
CivicOption=CIVICOPTION_GOVERNMENT, Civic=CIVIC_ANARCHISM
CivicOption=CIVICOPTION_RULE, Civic=CIVIC_OBEDIENCE
CivicOption=CIVICOPTION_POWER, Civic=CIVIC_STRONGMAN
CivicOption=CIVICOPTION_SOCIETY, Civic=CIVIC_PRIMITIVE
CivicOption=CIVICOPTION_ECONOMY, Civic=CIVIC_COMMUNALISM
CivicOption=CIVICOPTION_MILITARY, Civic=CIVIC_MILITIA
CivicOption=CIVICOPTION_RELIGION, Civic=CIVIC_IRRELIGION
CivicOption=CIVICOPTION_WELFARE, Civic=CIVIC_SURVIVAL
CivicOption=CIVICOPTION_GARBAGE, Civic=CIVIC_NOTRASH
CivicOption=CIVICOPTION_IMMIGRATION, Civic=CIVIC_NOBORDERS
CivicOption=CIVICOPTION_EDUCATION, Civic=CIVIC_IGNORANCE
CivicOption=CIVICOPTION_LANGUAGE, Civic=CIVIC_NO_SPEAK
CivicOption=CIVICOPTION_AGICULTURE, Civic=CIVIC_NOFARM
CivicOption=CIVICOPTION_CURRENCY, Civic=CIVIC_NO_CURRENCY
CivicOption=CIVICOPTION_LABOR, Civic=CIVIC_UNORGANIZED
Handicap=HANDICAP_NOBLE
EndPlayer
So barbarian is on 45 not on 49/50 as you told here problem or bug for you? And 3 times green man? Looks like a bug... looks like the mod saves it wrong... yep tryed to loading this new created scenario with the latest SVN, cant load it bug... so your MOD saves the NPC civs totaly wrong into new created scenario files...
Load the MOD then select PLAY NOW, then go to WB, then save the scenario... then look into the scenario with editor and look how it have been saved...
Ah Insectoids are on 45... hmm then the barbarian civ is missing completly?
Also i think there will be the problem for old scenarios to load because they miss:
BeginPlayer
Team=40
LeaderType=NONE
CivType=NONE
Color=NONE
ArtStyle=NONE
Handicap=HANDICAP_NOBLE
EndPlayer
BeginPlayer
Team=41
LeaderType=NONE
CivType=NONE
Color=NONE
ArtStyle=NONE
Handicap=HANDICAP_NOBLE
EndPlayer
BeginPlayer
Team=42
LeaderType=NONE
CivType=NONE
Color=NONE
ArtStyle=NONE
Handicap=HANDICAP_NOBLE
EndPlayer
BeginPlayer
Team=43
LeaderType=NONE
CivType=NONE
Color=NONE
ArtStyle=NONE
Handicap=HANDICAP_NOBLE
EndPlayer
BeginPlayer
Team=44
LeaderType=NONE
CivType=NONE
Color=NONE
ArtStyle=NONE
Handicap=HANDICAP_NOBLE
EndPlayer
Last but not least... the barbarian civ is missing and not saved in scenario file, maybe you have them on civ 50 but there are only civ 0-49 or you miss them now... cant also load any new created scenario.
6 NPC but only 5 NPC saved in new scenario file... <!-- 50 = BARBARIAN_PLAYER was 40 - Barbarians --> is missing or overwirting the insectoids. No NPC civ is saved on team=44 if you have 6 NPC, but there it should be saved.