In Altium (at least in version 14) when I create a PDF I don't see the pads. I generally create outjobs to produce PDFs of the PCB that have different copper layers on each page, essentially a PDF of the Gerbers. But through-hole pads which are multilayer don't appear on the top or bottom layers.
This is an example of what I mean. Here is what the PCB looks like in the layout editor:
And this is is what the PDF looks like, top and bottom:
I would like the option to show the pads so I can confirm connectivity, etc. without needing to use a Gerber viewer. I can change the color of the 'Multi-Layer' layer in the PCB Printout Properties in the Preferences window, e.g. to red, as shown below, but then the pad appears red on all layers, instead of blue on the bottom layer and red on the top layer.