The /problem/ is that other aliens are attacking you, while you're attacking a bk (IE: You maybe attacking a bk, but they'll probs be 4-5 sk's attacking you).
To be perfectly honest, I don't really see the point in using a bot to kill NPCs, collecting boxes is one thing, as its boring, but killing NPC is pretty much the secondary point of the game.
Config kBot to attack everything in the map, So once it finishes a BK, it'll go for the SKs, and it maybe an idea to set kBot to repair at a percent of like 50% or something if you're being popped a lot.
It all depends on your ship though, a FE ship isn't going to have as many problems as you are, and depends on the ammo you're using, So maybe stick to lowers for a bit, or just bot for uri for few days to get FE / Bio.
In GG, It's a little different, and personally for me, It completes the GG perfectly fine except in gamma, but if you're using it in GG, be sure to know when to come out and change config (IE: For prots, you'll want more engines, than for sibs; for example)
regards