Hi @spiny11 ,
I'm guessing that you defined the shuffled formula in a similar/same fashion as what's described in the online help you had the link to. I've had this happen to me before using the simulate option. Typically, I've been able to get it to go away by closing down the report window and trying to re-run the analysis. I think JMP occasionally gets a hiccup and the simulate feature doesn't work as intended.
Are you able to share your data table so others can see if they can reproduce the issue?
Good luck!,
DS