By default, PADS copies the pad from the top layer or bottom layer to the top solder paste and bottom solder paste layers, respectively. I believe it does the same on the solder mask layers after applying an oversize parameter that you can set. This lets PADS work with partially defined decals so it is a really handy feature for the newbies.
Once you have the SM and paste layers defined in the padstack, make sure those items are getting called out in the Gerber/CAM setup. If there is something defined for that layer then PADS won't take the shape from the copper layer and use it as a default, so if you don't define exactly what needs to go in the CAM definition you'll get nothing.
That's probably as clear as mud but it is really odd to describe. You'll have to play around with your CAM setup.
Thanks - it appears that the CAM document definitions for the solder mask and paste mask were somehow corrupted. I deleted those files and then added new ones (with the exact same configurations), and they worked just fine!