This "problem" isn't a problem at all but the system script is actually missing an important line. I've found that out when I was making slipstream.
This happens only in systems which do not have a "Player Start" waypoint in the system file. If you were to check the slipstream code you'll notice it's designed to use the "Player Start" navpoint also and will make a compensation for sets which do not have a "Player Start" Location.
So, all you need is something like this in the system file (usually scripts\systems\myset\myset.py):
# Position "Player Start"
kThis = App.Waypoint_Create("Player Start", sSetName, None)
kThis.SetStatic(1)
kThis.SetNavPoint(0)
kThis.SetTranslateXYZ(-3.792000, 0.000000, 0.000000)
kForward = App.TGPoint3()
kForward.SetXYZ(0.417716, 0.620277, 0.663905)
kUp = App.TGPoint3()
kUp.SetXYZ(-0.898685, 0.389602, 0.201435)
kThis.AlignToVectors(kForward, kUp)
kThis.SetSpeed(25.000000)
kThis.Update(0)
kThis = None
# End position "Player Start
Even some stock systems are missing this. This "problem" has been around since the start of BC.