To reproduce
1. Create 2 menu blocks. I position 1 in the header and one in the footer.
2. Change the "Number of levels to display" in the header version.
3. Review the footer block settings. The setting will also be changed there.
I do have menu_block module installed in addition to the system menu block. I wanted the ability to be able to create menu blocks with a parent menu item related to the current item.