This is one of those problems that is a feature, not a bug.
remember, one feature of the Newfangled suite is that you can string together several procedures into one big gcode file. If you are doing that, you would not want a spindle on command and tool change in each process. So the wizard looks to see if this operation is using the same tool as the last one, if so it does not include the spindle code.
Thats nice, but if its the first operation, and the tool is tool 0 (zero) then the program gets confused and doesn't turn on the spindle. I fixed this by setting the current tool variable to -1 in the init.m1s file, which runs when the wizard starts up.
If you are seeing this problem I guess you are using tool 0 and running an old version of the wizards.