Homunculi's flee rate seems to be really funny. Mine has trouble dodging 1 monster. The display window was bugged since RE to not apply the level bonus to flee(A level 99 homun would have 99 more flee than what it says in the window).
I think what might have happened is when you guys tried to fix this, you matched the homun's flee to the display window, rather than matching the display window with the real flee rate of the homunculus.
Another possible side effect: (Theory mode) now the flee rate is what exactly the homun window has. For instance: FLEE = Level + Level/10 + AGI (Lvl 99 + 9 + let's say 110 AGI = Flee 218)
Before, that number used to be wrong, just a number shown by the bugged homun window where the real number would be kinda +100 than the shown value. Now the flee rate shown by the homun window is THE REAL flee rate.
I just tested this theory with my Lv99 Lif (Flee 202) vs. Orc Warriors and Orc Ladies: She dodged the orc warriors quite often but the orc ladies hit her very often.
That's what I was having in mind.