yes, I think the agent may be technically correct.....but in practice, there is no time to re-weigh the bags for the second leg of the trip...they will be checked through all the way to MNL, with priority tags on them as well
the only way I could possibly be caught is if the agents in SFO enforce the rules. But they will most likely just check the bags dont exceed 2x23kg.
thanks for your replies.