Way back when I used to use Bobcad, I remember this problem. In short, it matters in what order you have either created the points for the hole locations, or else it matters how, and in what order, you selected them. "Select all" tends to "remember" the order in which they were created in, so although that is the quick function to use for select, it is not necessarily the best result, as you now know.
First you get good, then you get fast. Then grouchiness sets in.
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)