This happens if you use tool 0. The wizards try to be clever and not do needless commands. They check to see if the last tool used is the same as the current one, if so it skips the M3 and M6 stuff.
I fixed this in most places, and have a couple more fixes in 2.83. I got stalled in testing it and have not finished. I will try to get it checked out and post it in a day or two. Most of the changes have to do with the new comp code.