I was trying all possible ways and nothing... I still have:
a) The Enthrallment of Bogis marked red in the end
OR
b) Middle castle without King's Flag
Sigh
Is there any chance that you could replay these quests to check the order?
BTW: You said you've completed Bogis Problem and THEN* marked all castles with king's flag? *then = after? I've checked that and when I have this quest already completed I do not have any options in conversation to put king's flag over any castle...