Leadership flags were always stage-based, ever since KBAP. The higher the level of the area, the more leadership you get from a flag. If I dig into my old russian KBAP manuals I will probably find the formula, but I think it was something like stage 1-6 (based on the level of the enemies), leadership - a random number between 4 and 16, so a stage 1 flag would give something between 4 and 16, and a stage 6 flag would give up to 96 leadership. Colors matter too. I also think it gives only even leadership bonuses (like 4,6,8,16, etc.)
That's if I recall correctly