The mobo can hold some charge in it's capacitors but after that it's on the battery to keep the clock going and the bios chip alive(depends on the mobo a bit but some do that). Did it happen any times when you left the pc off for longer than normal?
Try not leaving anything plugged in to the USB ports while it's turned off for a while. I had a problem for a while of a usb extender causing the cmos battery to drain if the computer was turned off for too long.
The mobo can hold some charge in it's capacitors but after that it's on the battery to keep the clock going and the bios chip alive(depends on the mobo a bit but some do that). Did it happen any times when you left the pc off for longer than normal?