I worked around this problem by doing the following:
t=[0:1:3];
mdl='jordanTest'
inports=createInputDataset(mdl);
inports{1}=timeseries([5,6,4,5],[0,1,2,3],'Name',inports{1}.Name);
inports{2}=timeseries([2,4,3,6],[0,1,2,3],'Name',inports{2}.Name);
inports{3}=timeseries([1,4,2,5],[0,1,2,3],'Name',inports{3}.Name);
in = Simulink.SimulationInput('jordanTest');
set_param(mdl,'LoadExternalInput','on');
in = in.setExternalInput(inports);
out=sim(in)
It seems as if the timeseries have to have the associated port names included.