If you mean it runs "inside" of Arc, but not as stand alone, would really suspect it is related to feature layers.
ArcGIS will on-the-fly create the feature layers for tools that require it for input, silently (if running within Arc). If you pick from the drop-down list, you never know if you are getting the layer or feature class itself.
The help on the create random points is not quite right, as it says Random points will be generated inside or along the features in this feature class. The constraining feature class can be point, multipoint, line, or polygon. Yet, immediatly next to it, says Data Type = Feature LAYER???? (what is it, can't be both)
The cost distance/path both say they need feature layer.
Hope this gets you going,
R_