Hmm, tricky. The BEC should drain that pack 1st, since it places a small, but significant load onto it- only reason for the other pack(s) to drain quicker would be a bad cell, different Mah/C rating, or perhaps if a fault occured and the other system ended up doing all the work without you realising it (you'd see a drop in speed though, so it would be obvious that there was a problem with one motor/esc).
If you paralleled the battery packs together though (UNSLOW balancer), then they would discharge at the same rate, and hit LVC together:
