Check the ISO SENSITIVITY SETTINGS in the Camera Menu. When set to OFF, the ISO remains at your preset value regardless of the light conditions. It ignores the conditions you set in its submenu.
When set to ON, it follows the limits you set in that submenu.
For Esample: In M-Mode, I just set ISO SENSITIVITY SETTINGS to OFF,, fixed ISO 800, shot out the back door, then in the darkened entrance way. ISO remained fixed at 800. Good!
NOW! If I want the ISO to vary in manual mode, I go the the CAMERA menu and set the ISO SENSITIVITY SETTINGS to ON. Then I set the limits I want it to observe in its submenu. Now the ISO varies according to the lighting conditions, subject to the limits I set for it.