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When the pen tool is active, you'll see several options in your options bar.

Option 1 allows you to draw a shape while drawing your path. Basically it's nothing but a solid color adjustment layer with a vector mask.

Option 2 allows you to draw only the path

You can't stroke a path if option 1 is selected, so this option will be grayed out. In most cases you will notice it immediately when you're drawing a shape, but if your foreground color is identical to the background color of the layer you're working on, you might think you're drawing a path, when you're actually drawing a shape. So make sure that option 2 is selected.