My shelf pin holes show up in the Shopbot link, but doesn't output them to the machine. They are 0.1969" (5mm) holes. I have a tool setup at that size marked as a drill operation.
My first thought was to change the tool to 0.1968". I have a 0.001" tolerance set. No joy - still not outputting the code for the holes. My next attempt was to create a rout.dado tool in that size, and see if that worked... Nope.
Sorry. my own oversight. I had forgotten that I had checked the "No Drilling" option on the last job. I love feeling like an idiot first thing in the morning!