Peter - thanks for your question. However, this Member Resources community is for non-product specific questions. I am going to move your post to the PADS Layout community where it will get much greater visibility by PADS users. Thanks for using the Mentor Communities.
In Layout go to <Tools><Options><Via Patterns>. Is the via you are using listed in the 'When stitching shapes' list box? If not, see if adding it helps.
If not it seems like a bug.