Hmm. It works for me. Which app version are you running?
I added these paths to a layer:
… then ran this script in the Macro window:
pathOp = GSPathOperator.alloc().init()
p1 = Layer.paths[0]
p2 = Layer.paths[1]
p3 = Layer.paths[2]
thePaths = [p1,p2]
otherPaths = [p3]
pathOp.intersectPaths_from_error_( otherPaths, thePaths, None )
Layer.paths = None
Layer.paths.append(thePaths)
… and this is what I got:
