I'd go back to your EDA software and verify that the locations have been exported as drilled holes to the PADS file.
I found that if I use a version 3 IDF file (rather than version2) the holes come through. Also, If the parts are not placed on thegrid in PADS it can create a rounding problem for the placementcoordinates, and then SW says there is an error and won't importthe file. If you open the IDF file in a text editor you can roundthose location coordinates manually, and then everything workswell.
if you still need help i have import a lot of
pcbs from Orcad and Altium Designer 6 . .