@sarbian with the latest MJ build (that you built for me...) I've encountered two simulation errors:

1. Procedural fairings do not count as decoupled for the stages they should be decoupled under (verified by having them decouple in the stage prior to the engine lighting, then removing them entirely--different dV values for that stage)
2. MJ seems to no longer understand "stage and a half" staging, where you ground-light your engine but also have boosters (that burn out before your engine does, and are decoupled then).

It seems a safe assumption that these are related, and that a decoupler doesn't properly remove dry mass from the simulation stack, etc.

Fixed in 4acc2ac

KER also shows different, slightly lower dV value than latest Curse release of MJ. Presumably because MJ is using 1.0.0 atmosphere and KER 1.0.2.