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I think that will be because you've given Lord Paramount titles to other lords. You need to hold the actual Kingdom titles (not Lord Paramount ones) and hold them all yourself.
 
Its in iron_throne_decisions in the decisions folder. Save the original file somewhere on your computer, just in case someone comes up with a better work around (mine is a 'brute force' method. Take out the decision (its the first on in the folder) and insert this...

decisions = {
create_e_iron_throne = {
is_high_prio = yes
potential = {
primary_title = { tier = EMPEROR }
e_iron_throne = { has_holder = no }
}
allow = {
war = no
}
effect = {
hidden_tooltip = {
primary_title = {
e_iron_throne = { copy_title_laws = PREV }
set_global_flag = non_iron_throne_westeros
set_global_flag = KL_not_capital
if = {
limit = { title = e_north }
k_north = { gain_title = FROM copy_title_laws = PREV }
}
if = {
limit = { title = e_riverlands }
k_riverlands = { gain_title = FROM copy_title_laws = PREV }
}
if = {
limit = { title = e_vale }
k_vale = { gain_title = FROM copy_title_laws = PREV }
}
if = {
limit = { title = e_westerlands }
k_westerlands = { gain_title = FROM copy_title_laws = PREV }
}
if = {
limit = { title = e_reach }
k_reach = { gain_title = FROM copy_title_laws = PREV }
}
if = {
limit = { title = e_stormlands }
k_stormlands = { gain_title = FROM copy_title_laws = PREV }
}
if = {
limit = { title = e_dorne }
k_dorne = { gain_title = FROM copy_title_laws = PREV }
}
if = {
limit = { title = e_iron_isles }
k_iron_isles = { gain_title = FROM copy_title_laws = PREV }
}
}
}
e_iron_throne = { gain_title = FROM }
hidden_tooltip = {
any_realm_lord = {
primary_title = {
dejure_liege_title = {
if = {
limit = {
tier = KING
NOT = { title = k_the_most_devout }
NOT = { title = k_nightswatch }
NOT = { title = k_beyond_wall }
OR = {
AND = {
OR = {
holder_scope = { character = ROOT }
holder_scope = { any_liege = { character = ROOT } }
}
dejure_liege_title = {
NOT = { title = e_new_valyria }
NOT = { title = e_ghiscar }
NOT = { title = e_summer_sea }
}
}
dejure_liege_title = {
holder_scope = { character = ROOT }
NOT = { title = e_new_valyria }
NOT = { title = e_ghiscar }
NOT = { title = e_summer_sea }
}
}
}
de_jure_liege = e_iron_throne
}
}
}
}
any_demesne_title = {
limit = {
tier = EMPEROR
NOT = { title = e_iron_throne }
NOT = { title = e_new_valyria }
NOT = { title = e_ghiscar }
NOT = { title = e_summer_sea }
}
destroy_landed_title = FROM
}
}
}
revoke_allowed = {
always = no
}
ai_will_do = {
factor = 0
}
}