So if you wanted a blue base layer, but red F1-F12 row, you add a static blue effect (entire keyboard turns blue). You are going to do that unintentionally more than once. If you simply left click anywhere in the field, the entire lighting effect is removed. To selectively apply or remove LEDs or groups of LEDs, you need to CTRL + left mouse click (single) or mouse click drag to box a group of LEDs. In CUE 3 the lighting effect is applied to the entire group the moment it is created. Once of the choices will be fixed RPM or fixed PWM %. If it were to happen again, you might be able to lift the front end of the case so the radiator is higher than the pump, allowing the air to travel to a less problematic place. A 5 year old unit is likely lower on fluid than it once was and that makes the air pocket in there larger and likely to cause a problem. There is no other good reason for block orientation to matter. It seems most likely you had some sort air pocket around the CPU block after the move. Neither pump nor fans is getting a PWM signal from the motherboard. It requires voltage, not a PWM signal from the motherboard. If you do it to the AIO, pump and fans slow down below minimum levels.
If you use voltage control within the BIOS (lowering it below 12v), it has the same effect as twirling a dimmer switch on the ceiling fan. The 3 pin is the main power to the unit and it needs 12v. Everything must work on variable voltage and not PWM mode