When it generated inside code at the start it moved to the center of the hole then out to a start point then BACK to the center of the hole then BACK to the startcut point before continueing.
Were you doing RH or LH thread, and did you set Climb or Conventional mill ?
The reason to go bottom up on outside thread is to allow conventional milling. If you want climb milling then top to bottom is Ok, for inside threads its the opposite. At least I think I got those combinations correct, I had to draw it all ot when I was working on the code, I think the code is right, I may be saying it backward now.
Im at Cabin Fever now so I cant look at the code to see about the tool table problem, Ill check it when I get home Monday night.