I created a footprint for a Xbee module.
The pads i created are multilayer but when i do a print job (smart pdf) the holes for the component are on the top layer.
When i change a pad to bottom layer, the pad is on the correct layer but i don't see the drill hole anymore.
I'm suspect the pdf converter. I suggest going to File/Fabrication outputs and generating Gerbers. You can down load View Mate from Penta Logic for free to view the Gerbers. Many designers always do this before up loading files for PCB fab as a check. In VM be sure to set the file type to All else you will not see the files.
You should also go to Design/Stackup Manager and check to see if the drill pairs are top and bottom.
I may be wrong but it looks to me that there are problems with the footprint for SD1 also, it looks as though the pads are set to be multilayer pads and have no drill hole set up. If you want to attach the PCB Library file or PCB file I'll take a look for you.