Julia, I wonder if this isn't just a case of being tripped up by incorrect effort conversion factors. You say you have a schedule of 8-5, but you don't say whether that includes the lunch hour or not. If you have a single block for 8-5, that's 9 hours, not 8, and the effort conversion factor is likely still set to the default of 8 hours, which matches the default schedule of 8-12 + 1-5.
I wrote a post a while back that helped some readers cotton to the way this works. It's in this thread
-- read it and see if that doesn't clear up the mystery. If it doesn't, I'll try again :-)