Some PSU's do not allow this, and some do, so that may be why you never saw it before on other boards or systems.
You can try disabling Wake from USB in the BIOS power page. It's a hidden settings, if you are on the latest BIOS, if not please update to the latest BIOS. Then on the MAIN page of the BIOS press control + F1, and the screen will flash, then go into power options and disable the wake from USB option and see if this stops that. If it does not then that means your PSU leaves the +5v line enabled while the system is powered off. This is a new feature in power supplies, made in the past 5 years or so, so devices can be charged via USB while the computer is off.
Pentium D is dual core Pentium 4, not core 2 or core 2 duo, it was made right before they made Core 2