New System and I have a proble,

So I have a new system and I have noticed and issue.

IT usually happens when I use the power switch on the front of the case, for reset. I hold down the system..... after turning it off I hit the button to reset the computer and the mobo led lights flash on and the fans blink on for a few minutes, my system is equiped with a fan only setting on the soft power switch which I am sure is causing the fans to kick in and run when the system is off like this, so I am cool with this.
The problem comes when I try to reload. My keyboard is a usb, and after a shutdown like this one the keyboard gets no power and is not recognized so I can't get into bios, and windows vista reports an improper shutdown which I have to wait for the countdown (because my keyboard is offline) then windows takes forever to load and essentially has to re-recognize all of my usb peripheries again. Including mouse, keyboard, and 2 external hard drives. When I am done, my windows clock is always 2 hours off as for some reason it really wants to be eastern time.

other than the minor inconvenience of the long load up, the issue isn't really that big of a problem especially since vista has a real nifty, low energy state that I generally use instead of shutdown, I am more concerned that this is the start of a bigger problem, that will end up damaging my system.

Has anyone else experienced this? or know something about it?