Brendan,
does the step up S-cab board lower run time? It has to be using more current to step the voltage up I would think, but it may be negligible.
It may not even matter to most. I get over 2-1/2 hours on my 2000 Mah, 9.6v packs in my O-scale engines, a 3.7v battery would be a no-go for me. That's barely enough to turn the LED headlight on.
It's odd that my G-scale 4-6-0 (with a BlueRail board and 12v, 2000Mah battery) can move out with a single tap on my IPad, but my WbB semi-scale 4-6-2 took a bit more "juice" to make it move. Must be the gearing, or it could be the difference between the 12v battery in the 4-6-0 and the 9.6v battery in the 4-6-2, maybe both!