Hello, we replied to your email 2 days ago, you have not sent us all the handhistories. However it seems like you figured out what is causing the difference in expected results.
As far as the formula goes, it has worked this way since HEM1 days, it has not changed.
It uses river pot size and opponents bet as the amount that can be won. So if river pot size is $3, and opponent bets $1, if you call $1 you will win $4 which will be your river efficiency $. In this case your river efficiency would be 4.
If it worked like you suggest, and it only looked at opponents bet size on river and ignored previous pot, then at most you could have river efficiency of 1 / $1. (Since at most you can only win $1 for opponents each $1 that he bets).
Here is one of the discussion on 2+2 if you would like to read more about it and how to interpret it:
River Call Efficiency - Micro Stakes Full Ring Games - Micro Stakes Poker Strategy Forum