I'm not sure if im qualified to answer this but I am learning the same stuff right now and I can tell you how I understand it. So let's take the example of (2E,4E)-2,4-hexadiene vs. (2E,4Z)-2,4-hexadiene. For the (2E,4E) version to get into it's s-cis conformation it costs less energy than for the (2E,4Z) because of the methyl-hydrogen van der waals repulsion in the (2E,4Z) version vs. just the hydrogen-hydrogen interaction in the (2E,4E) version. In other words the equilibrium constant between the two conformations is larger for the (2E,4E) version. Therefore at any given time you will have more of the (2E,4E) s-cis conformer to react making it the faster reacting isomer.
Attached is a pretty good picture Loudon gives.