Salutations,
Labview 6.0 eh? Kicking it old school, I like that.
Well, normally auto-scaling doesn't go straight to the lowest value, it normally gives you a bit more space, for visualization purposes, I'd imagine (by 5.0, i'm assuming you mean 5.0e-9). Also, if any value is around that size (5.0, not 5E-9), for whatever reason, it will include it. Hence, if you only have 1 point of 5.0 and everything else is 1e-9, then it will use 5.0 as the max.
Hopefully, 6.0 has the ability to create property nodes. If you're capable of doing this, create a property node to the graph, select Y min or Y max, or Start, you know, whatever makes you happy. After you've made the selection, wire the value that interests you. This could be done by pulling out the min (using the min/max function) and then wiring the min or max to the graph. Then it will use your 1E-9.
Also, if you're using two axis to plot, make sure you're "connected" to the proper axis.
Sincerely,
ElSmitho