Ok, there's nothing wrong in the registers.
Regarding CSEc and EEE:
lukaszadrapa_0-1685432699263.png
Also the device can't run in high speed mode:
lukaszadrapa_1-1685432736387.png
Notice that SDK drivers do not check if EEE/flash operation is running when CSEc functions are going to be executed. I was already asking for this but it is not implemented yet. Currently it is up to user to check this.
Regards,
Lukas