I see 2 things for you to look at.. I only looked at the first advanced rough in the list.
First, review the tool size and be sure it fits where you want it to go.. The gold cylinder is the tool listed in this feature:
Second, the rough toolpath will look at the set steps, and stop if the last step doesnt fit. here I set the toolsize to 4, then entered a value in the "number of intermediate steps" field... This field gives the toolpath a calculation of how many steps it can use to puch against this... Here I entered 10:
Although with a tool of 4 and intermediate steps calculated at 10, the toolpath is still slightly off the bottom... I need to look to see if there is a number that can be derived from the math, to push it to the exact bottom. But it IS a roughing toolpath, so I'm not sure yet.