I've found a temporary fix to the colony system in 2.02b:
change all wait 1 to wait 0.1
and do:
monitor_event FactionTurnStart FactionType f_pergamon
wait 2 ;make sure there is no leftover monitors from previous turn
if I_CompareCounter PergamonColonyPoints > 0
set_event_counter ecPergamonColonistsOn 1
end_if
end_monitor
to all 9 factions.
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However, something else is confusing me:
when I try to replace
monitor_event FactionTurnEnd
if I_EventCounter ecMakedoniaColonistsOn <= 1 ; the event is off or on
set_event_counter ecMakedoniaColonistsOn 1 ; enabling the event counter to allow construction to continue
wait 0.1 ; stop processing this monitor for x.x seconds
set_event_counter ecMakedoniaColonistsOn 0 ; disable\reset the event_counter for the next round, if colonypoints counter is > 0 then this will be set back to 1 at faction turnstart
end_if

with:
monitor_event FactionTurnEnd
if FactionType f_makedonia and not FactionIsLocal ; the event is off or on
set_event_counter ecMakedoniaColonistsOn 1 ; enabling the event counter to allow construction to continue
wait 0.1 ; stop processing this monitor for x.x seconds
set_event_counter ecMakedoniaColonistsOn 0 ; disable\reset the event_counter for the next round, if colonypoints counter is > 0 then this will be set back to 1 at faction turnstart
end_if
end_monitor

the colony system breaks at turn 1, which doesn't make any sense to me because they are endturn monitors and no endturn has happened at turn 1.