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.
I suspect it does. Encore's transcode engine is from the sonic core, and does not take advantage of adobe media encoder. (Even if that option is selected, it is only for "transcode now" - meaning timelines.) With H264 timelines, encore must decode before generating the new menu background and then transcoding.
Did you see any difference as makdm1 in the menu durations?