Slow shutdown Z87-GD65 Gaming

If I allow my Win64 system to go into sleep mode. Wake it up and then try to shutdown I find that it takes ages to shutdown once the black screen appears. It seems like it has shut down but the fans keep spinning for a good 20 seconds and eventually I will hear my speakers pop as the soundcard powers down. A reboot and then power down does not take anywhere as long. Regardless of what apps have been running or are running.
I also get random DPC latency spikes if I do not reboot after going to sleep or even just running on 'balanced' for a while. Setting power management completely off and rebooting resolves this.
Is this more likely to be a USB device causing the above issues?
I am using BIOS E7845IMS.1A3

Board: MSI Z87-GD65 Gaming
Bios: Version 1.10B E7845IMS.1A3
VGA:   Sapphire Radeon R9 290 Tri-X 4096MB GDDR5 PCI-Express Graphics Card (11227-03-40G)
PSU:   EVGA SuperNova G2 1000W '80 Plus Gold' Modular Power Supply (12v 83.3A 999.6w)
CPU: Intel Core i7-4770K Haswell 3.5GHz (3.7GHz Turbo Boost) LGA 1155 84W
MEM: Corsair CMZ16GX3M2A1600C9 Vengeance 16GB (2x8GB) DDR3 1600 Mhz CL9 XMP Performance Desktop Memory Kit Black
HDD: Samsung 840 EVO Pro 256GB SSD, Samsung F3 1TB x 2, Samsung F3 2TB x 1, Seagate 500GB
COOLER: Corsair Hydro Series H90 140mm High Performance Liquid Cpu Cooler
OC: No
OS: Windows 7 64bit Professional
Connected USB peripherals
Seagate Desktop 2TB USB 3.0 HDD
Seagate Desktop 4TB USB 3.0 HDD
Logitech G15 Keyboard
Logitech Revolution Wireless Mouse (Wireless adapter on G15 Port)
Novation Twitch DJ Controller
Epson Stlyus Printer (Off)
Other
3COM U.S. Robotics Message Pro Fax Modem on Serial port 1
Suggestions on what to try first?

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