It seems to depend on what you're doing. Plus, the delay I needed turned an already slow animation in to a slide show.

In this case, a better fix seems to be sticking a "root.update()" right before the "root.after". Then it works with no delay. However, apparently it's a little dangerous to use:

http://mail.python.org/pipermail/tkinter-discuss/2013-January/003346.html

In my case, the only side effect seems to be that using the menu effectively pauses the simualtion.