When using the kerbalCrewMass global physics variable, the vessel mass seems to be calculated incorrectly while in the VAB. Instead of adding the number of kerbals and multiplying by kerbalCrewMass, it seems to be doing this per part. This only seems to happen in the VAB, and I don't know if it affects the DeltaV readouts yet. Interestingly, KER seems to experience the same bug: http://forum.kerbalspaceprogram.com/index.php?/topic/17833-121-kerbal-engineer-redux-1128-2016-12-02/&page=152#comment-3003230
I had actually thought at first that it was a stock bug, and opened up this report: http://bugs.kerbalspaceprogram.com/issues/14679

kerbalCrewMass isn't referenced in any way by MechJeb at all.

Whatever is causing it, it's not this mod.

Just did some additional testing and it is most definitely a stock bug. Bewing is wrong; kerbalCrewMass is most definitely implemented. And it does NOT just affect the mass reported in the VAB.

It affects real vessel mass in the Flight scene. You can check this by setting kerbalCrewMass to something ridiculously high and watching your vessel's TWR be affected in flight mode. Or if you set it high enough it might not even be able to lift off (kerbalCrewMass = 50, put a Mk1-2 Pod on top of the largest SRB and put it on the pad). Or set it to something really outrageous like 500000 and watch your vessel demolish itself on the launch pad.

Closing this as an old MechJeb issue. Many MechJeb issues have had little interest in years, have been fixed for years, do not include adequate replication steps, refer to old problems which are no longer applicable, or are difficult to determine what the problem is. This issue is being closed for one of those reasons. We apologize for any inconvenience, but keeping the TODO list tidy helps the developers.

If this bug/issue is still a problem, please open a new issue. For bugs please try to include a Minimal, Complete, Verifiable Example that explains all the steps required to replicate the issue. A link to the KSP.log file should be ideally included, but is often not sufficient information. Screenshots or short videos are often the best way to show a bug.