The new mobo must have power on via mouse and keyboard enabled. It powers the mouse and keyboard using the +5V standby while the rest of the computer is off.
The on-board LED is also probably powered via the +5V standby, just to remind you that it's plugged in.
Did you reformat and reinstall windows when you installed your new mobo? Windows often acts funny when you do a mobo swap. It's better to reformat and reinstall windows when changing mobos.