I don't know if this will help you or not. I'm getting pretty rusty on Bobcad these days. But, it seemed to me that when you were pocketing you picked the profile and then the islands (the bosses you speak of). The location of the cursor when you picked the islands was critical to the outcome you got for a toolpath. Make sure your cursor is on the outside of the islands. Even then, you need to watch where you place the cursor before you "click it" to select an island. If you have more than one island, you may need to experiment a bit with various cursor locations to get a desirable outcome.
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)