That diagram of the clocking system is a good example of how the bigger MCUs are like having a whole computer on a single chip, with all the implications of complexity that brings. It's not enough to set up a single clock; you also need to make sure the clocks to the peripherals that are in use are also what you need them to be.

(I wish such diagrams in datasheets would let you click on the appropriate blocks to jump directly to their registers and description sections.)