I have made sure my settings were what the guys at Precomposed recommended (MPEG-2, 1920x1080, 29.97fps), but still got poor results rendering the motion menus in Encore.
This was the response I got from Precomposed:
Unfortunately Encore is not the most efficient rendering application. Several factors cause it to take much longer to render in Encore, such as the number of scene boxes per page, and the codec of your main video. Despite it taking a little more time to setup in After Effects, I highly recommend that method over using Encore to render video into the scene boxes. If this creates too much work for you, you may want to consider reducing the number of chapters so you only have a page or two to configure.
I don't think the codec of my main video (which is h.264) makes a difference in the speed of the motion menus rendering, but who knows. Anyway, his answer didn't offer any other suggestions. Just that I'm basically better off rendering everything in After Effects.