Are they both the same brand battery? Do they both have the same number of cycles on them? Different brand LiPos could perform differently from one another even if they have the same IRs. 10mOhm is generally where I start using the packs for lighter duty loads though.
Even if they are the same brand with the same IRs, If one pack has more cycles on it then that could cause it to have less mAh than a pack with less cycles.
Also the BLX100 ESC which I believe is what the Big rock comes with, has very little programmability. Now I dont know if theyre anything like the Spektrum 160A ESCs but the LVC on those ESCs can only be set to "Auto - High", "Auto-Medium", or "Auto-Low". One thing I noticed when using that ESC is that the LVC never seemed to kick in at the same level. it was always a bit different. That may be comparing Apples and Oranges though as IDK if Spektrum even makes the BLX ESCs.