[Help] Very Odd Power Down Issue

I have a 4 year old computer I bought from ABS that is behaving very odd during shutdown. When I shut the computer down via windows, instead of turning off and going silent, it now produces a high-pitched whining sound while powering down. All the fans continue to spin and all the lights in the computer, and the drive activity lights, flash rapidly. The fans and the lights then begin to spin and flash progressively slower over the course of about 15 seconds, after which, the computer is finally off.

This is a new issue, and I'm wondering if anyone has any experience with something like this? Is the power supply the problem, or is the motherboard at fault? I don't use this computer that much anymore, but I'm afraid one of these times, when I shut it down, it will fry a component and not come back on.

Any help is appreciated.

Thanks for the reply, but I just did a complete reinstall of windows on it and the same thing still occured on a fresh windows install.

Not only are my HD lights flashing, but my dvd-rom activity lights, as well. My fans also continue to spin after the computer is off and slowly spin down till they stop on their own.