That small light that is always on is probably just indicating that power is available to the motherboard.
How is it that you are seeing a light inside the case on the motherboard?
Take a photograph or two of the light and post here using imgur (
www.imgur.com).
Not sure that I fully understand the circumstances/arrangement of things.
= = = =
Powering off via the PSU is not good for the system.
Three suggestions:
1) Install a new CMOS battery
2) Run "sfc /scannow" and "dism" to find and fix any corrupted files.,
References:
https://www.lifewire.com/how-to-use-sfc-scannow-to-repair-windows-system-files-2626161
https://www.windowscentral.com/how-use-dism-command-line-utility-repair-windows-10-image
3) Use the normal Windows shutdown icon for a few days and allow Windows to catch up on its' "housekeeping" (updates, saving settings, etc.) Thereafter, once the normal shutdown is complete then you turn off power to the PSU/host computer.
Also, again, just try putting some other object in the line of sight between you and the annoying light. Maybe just a piece of dark paper to cover the light but do not block any ventilation holes.