Check that the two line and/or polygon layers you are using have the same projection (spatial reference).
If not, you will need to reproject one to match the other.
Which layer to specify first?
It does not matter which layer you use as the "Line/poly layer" and which you use as
the "Intersect line/poly layer" UNLESS you want to copy attributes to the output points.
In this case the layer you specify as the "Line/poly layer" is the one from which
attributes will be copied.