With a fuelline going into a decoupler it's possible to make a decoupler not block the stackfuelflow anymore so upperstage radial engines can be fed from lower stage fueltanks.
But MJ doesn't know that yet so it assumes the fuel is actually used up later than it is actually.

In the given screenshot the time of stage 5 increases when I activate the upperstage engines (although that doesn't happen like that at launch but it's just for showing it).
With the upper 4 engines added the vacuum time goes up to 970 because it assumes the fuel is used up above.

OK, I bet cb39326 will fix this. Could you try it out in the latest dev build?

I'll try to look into this later, but it's possible that bce6ca5 fixes this already. If you want to could try the dev build at http://jenkins.mumech.com/job/MechJeb2/ and see if it works correctly.

Doesn't seem to be fixed from that, I still get the 970 from before for stage 5.
http://img441.imageshack.us/img441/3018/screenshot1wop.png
http://img825.imageshack.us/img825/5036/screenshot2fb.png

Yeah, this seems to work, when I toggle the upper engines only the lower dV changes, the upper stays the same like it should.