Setup - User Preferences - Paths - Library - padpath is the location of where you store pads (filename.pad). Make sure any vias you want to use are stored in this location. The Modify Padstack list will only show pads that are used in a design, You can launch Padstack Editor as a stand-alone tool from the start menu and edit / add the pads you need, then store them in the padpath location. You can then add them to your via list.
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