Thanks for the support group mentality, now I don't feel quite as frustrated with this game :)
My problem with the flee percentage is that, they're not fleeing when its 20% they're fleeing when the shields are perfectly fine. Now it could be coded such that damage = bad therefore override all shield IF statements and run away, it could be that if the shield penetrating damage occurs there's a glitch in that it thinks the shields must be zero if damage occurred therefore run. My Ship Battle Caution Factor is set to Low, and still my capital ship (which mysteriously disappeared from last nights save game to this morning... but that's another issue) still run away with 1 damage.
So until they fix things with this I have a few ideas to run by.
1. Set to never run away is the easiest, but might be the most costly. Also not sure if that priority will stay even if the AI automatically upgrades ship designs, could be extremely tedious/game breaking if I have to keep changing that.
2. Mod out all shield penetrating weapons or their effects. This is a more brutal and game changing fix, but I really don't want to play any more as a result of this. A cruiser is harassing a colony I'm trying to grow, 1 on 1 with my capital ship it has zero chance of winning, however it keeps running away when it's shields are at 20%, then comes back very shortly after usually to run away again when the first missile hit knocks it's shields back below that 20%, now as annoying as this is I can deal with it until backup fleet comes back. However that cruiser managed to hit me with a gravity weapon my shields are still strong as ever but that 1 damage makes him run away, cruise destroys the base I was building, and anything in the area. Sorry, that's not acceptable.