I updated the settings to the blocks when I ran the Schedule Maker. Now, Schedule Maker is ignoring the blocks courses can use.
This is because of the settings you selected when you ran the Schedule Maker.
At the very bottom of the Start Schedule Maker screen, there is a box called "Which settings should be followed?" You would need to unmark the box for "Blocks courses can use" in order for the Schedule Maker to follow the block settings you set for the courses.