I'm throwing stuff out here that I've actually had problems with at some point
 
If you folks have USB interfaces, make sure you check out other USB devices in your system.  I've had things like keyboards make my system flaky.  On my system, if I swap other devices around in USB ports I can get errors until apps figure out where the heck everything is.  By other devices I mean other than audio interface, so I wouldn't normally think of them causing problems.
 
Make sure everything USB is set to stay on always in power management options.
 
I've also had weirder stuff happen ... USB devices that work fine when in plugged into one port, but not others.  Move USB things around.  Also, all USB 3.0 ports are not created equal.  Especially when it comes to backwards compatibility with USB 2.0 devices.

BobF
Also, all USB 3.0 ports are not created equal.

This is SO true. The RME site has a detailed description of what hoops you have to go through to use their MADI USB 3 interface. The following is just the "short form," there's MUCH more detail in the manual.
 
The special features and possible problems of using USB 3 are described in more detail in the manual.
 
Current Compatibility Information:

• Fully compatible to Intel's USB 3 implementation, which - on current Windows and Mac computers - is part of the chipset. USB 3 sockets that are connected via an internal cable (not directly soldered onto the motherboard) can cause transmission errors. These are shown in the Settings dialog.
• Fully compatible to AMD's USB 3 implementation. USB 3 sockets that are connected via an internal cable (not directly soldered onto the motherboard) can cause transmission errors. These are shown in the Settings dialog.
• Fully compatible to Fresco USB 3. This rarely used chip can be found for example on the Sonnet Tango 3.0 PCIe card.
• Compatible to NEC / Renesas USB 3. Real-world performance and error-free operation depend on the firmware version, driver version and the PCB layout of the respective extension card/motherboard.
• ASMedia - not compatible.
• Etron EJ168A - not compatible.
• Texas TUSB7340 - not compatible.
• Via VL800/805 - not compatible.

Something that has been helpful to me when encountering a similar situation was to turn off the audio engine (Blue button on the transport) before shutting down.  This should stop any lingering output (infinite reverb?) from keeping your audio drivers busy past the shutdown.
 
If this makes a difference, you may want to examine your VST settings and Sonar settings a bit more closely.
 
Glen

This happened to me about a month ago, and it turned out to be a bad hard drive.  Specifically, my E drive where I store my projects.  Once I replaced that, all problems went away.