MechJeb is incorrectly computing the dV for vessels with engines that have "Drains stage-by-stage, balanced" fuel usage (including all jet engines, but also the R.A.P.I.E.R. engine even in closedCycle mode) in cases where the engine would not otherwise have access to all fuel on the given stage. For example, in this craft, the engines can and will drain the Mk3 tank, but MechJeb does not recognize this:

Adding fuel hoses (from Mk3 fuselage to radially-mounted tanks) solves the problem.

Craft & log files:
MJ Bug 2.craft.zip
KSP.log.txt