A strange issue kept happening where our CAM patterns wouldn't respect the settings inside to "Order by Tool" (see image below).

Reason / Solution

The sub-folders used to organize operations are causing the pattern to disallow the parent pattern. It doesn't really make sense but this is the reality. The two red arrows point that out and cause tool changes because it runs through the operations one by one instead of by the tool at each position. The green arrow below works just fine and as expected.

TLDR - Remove subfolders inside a pattern.