Some newer psu's have a "cooldown" feature thats continues running the motherboard fans to cool things down, before shutting off completely in a few seconds. Some motherboards also have this feature in the BIOS. Recently built a system that had both cooldown features and they "fought" each other for control; causing strange stuttering etc at startup/shutdown. Disabling the feature in BIOS solved the issue, by allowing only the PSU to control the Cooldown feature.
Your PSU (in sprcs), Enermax Infiniti 650W, has this feature; CoolGuard: The new patent feature, running not only PSU fan after shutdown, but all system fans to get the heat out of the system and increasing system lifetime by up to 20%.