So the difference is in the active device?
I suspect that some amount of inductance is included in the HBT S-parameter data -- whatever they used during measurement to create the ground path. If you now include the full ground path in EM, you might over-estimate inductance in that path (your layout's ground path L + HBT S2P measurement ground path L).
So maybe you can go to circuit simulation and tweak some +/- delta L to see how that affects overall results.