I'm using trunk version 8667 of gazebo through libgazebo. I think there's an error in the computation of the nsec part in SimulationRequestData::GO in server/world.cc (introduced while fixing bug 2923653):
int nsec = (req->runTime - sec) * 1e9;
should be:
int nsec = (req->runTime - sec*1000) * 1e6;
I've attached a patch that fixes it.
patch fixing error computation nsec part Simulation::GO request in world.cc
Revision 8678 has partially solved the problem. In that revision sec is multiplied by 1000 before subtraction. However, the remainder is still multiplied by 1e9 which should be 1e6 since runTime is given in miliseconds.
Fixed in revision 8684